I wrote:
...
> 2.6GHz Opteron (Tyan Quad-opteron TX46 mobo)
> 64bit
> =====
> anneal: 553.428u 17.660s 9:31.32 99.9%  0+0k 0+0io 0pf+0w
> rigid: 44.194u 1.139s 0:45.35 99.9%    0+0k 0+0io 0pf+0w
>
> 32bit
> =====
> anneal: 410.701u 17.245s 7:08.15 99.9%  0+0k 0+0io 0pf+0w
> rigid: 28.063u 1.079s 0:29.15 99.9%    0+0k 0+0io 0pf+0w
>
> 32bit-g77
> =========
> anneal: 596.445u 17.163s 10:13.88 99.9% 0+0k 0+0io 0pf+0w
> rigid: 75.080u 1.136s 1:16.31 99.8%    0+0k 0+0io 0pf+0w


upon inspecting the table again I found that I'd made a cut-and-paste
error - the last line was wrong. Opteron 32bit-g77 rigid should be:
rigid: 46.446u 1.055s 0:47.52 99.9%    0+0k 0+0io 0pf+0w

To repeat, this was the g77 binary from the CNS distro as obtained from
the asdp.bnl.gov site, dated Aug 18  2003 - but I don't know what
version of the compiler that was.

Kay
--
Kay Diederichs              http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs@...  Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

Hi All,
Any thoughts of speeding it up with 64 bit mode? We have a direct
rotation inp that is
going on for 25+ days and I was hoping to get a speed increase on the
Opteron
without success so far!
I tried the couple of postings with different flags but did not help.

Thanks

Balaji


Kay Diederichs wrote:

>I wrote:
>...
>
>
>>2.6GHz Opteron (Tyan Quad-opteron TX46 mobo)
>>64bit
>>=====
>>anneal: 553.428u 17.660s 9:31.32 99.9%  0+0k 0+0io 0pf+0w
>>rigid: 44.194u 1.139s 0:45.35 99.9%    0+0k 0+0io 0pf+0w
>>
>>32bit
>>=====
>>anneal: 410.701u 17.245s 7:08.15 99.9%  0+0k 0+0io 0pf+0w
>>rigid: 28.063u 1.079s 0:29.15 99.9%    0+0k 0+0io 0pf+0w
>>
>>32bit-g77
>>=========
>>anneal: 596.445u 17.163s 10:13.88 99.9% 0+0k 0+0io 0pf+0w
>>rigid: 75.080u 1.136s 1:16.31 99.8%    0+0k 0+0io 0pf+0w
>>
>>
>
>
>upon inspecting the table again I found that I'd made a cut-and-paste
>error - the last line was wrong. Opteron 32bit-g77 rigid should be:
>rigid: 46.446u 1.055s 0:47.52 99.9%    0+0k 0+0io 0pf+0w
>
>To repeat, this was the g77 binary from the CNS distro as obtained from
>the asdp.bnl.gov site, dated Aug 18  2003 - but I don't know what
>version of the compiler that was.
>
>Kay
>
>

Dear all,

Since severall days we filled the form of the CNS distribution web page
but no mail is sent back and so we don't get the password.

Does somebody know what is happening ? What should we do for getting CNS ?

Thank you in advance,
Cheers.

Vanessa DELFOSSE.

and I am receiving this error. Can someone please help me

xrmani.f: In subroutine `xgene2':
xrmani.f:801:
          SUBROUTINE XCOPY(ARRAY,REFLCT,CTEMP,REFLCT2)
                     1
xrmani.f:1252: (continued):
          CALL XCOPY(HEAP(HPSF(I)),XRNREF,DCMPLX(ZERO,ZERO),1)
               2
Argument #1 (named `array') of `xcopy' is one type at (2) but is some
other type at (1) [info -f g77 M GLOBALS]
xrmani.f:817:
          SUBROUTINE XCOPYR(ARRAY,REFLCT,TEMP,REFLCT2)
                     1
xrmani.f:1255: (continued):
          CALL XCOPYR(HEAP(HPSF(I)),XRNREF,ZERO,1)
               2
Argument #1 (named `array') of `xcopyr' is one type at (2) but is some
other type at (1) [info -f g77 M GLOBALS]
xrmani.f: In subroutine `xexpa2':
xrmani.f:801:
          SUBROUTINE XCOPY(ARRAY,REFLCT,CTEMP,REFLCT2)
                     1
xrmani.f:1960: (continued):
          CALL XCOPY(CTEMP,1,HEAP(HPSF(I)),REFLCT)
               2
Argument #3 of `xcopy' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f:801:
          SUBROUTINE XCOPY(ARRAY,REFLCT,CTEMP,REFLCT2)
                     1
xrmani.f:1963: (continued):
          CALL XCOPY(HEAP(HPSF(I)),XRNREF,CTEMP,1)
               2
Argument #1 of `xcopy' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f:817:
          SUBROUTINE XCOPYR(ARRAY,REFLCT,TEMP,REFLCT2)
                     1
xrmani.f:1972: (continued):
          CALL XCOPYR(HEAP(HPSF(I)),XRNREF,HEAP(HPSF(I)),REFLCT)
               2
Argument #1 (named `array') of `xcopyr' is one type at (2) but is some
other type at (1) [info -f g77 M GLOBALS]
xrmani.f:817:
          SUBROUTINE XCOPYR(ARRAY,REFLCT,TEMP,REFLCT2)
                     1
xrmani.f:1972: (continued):
          CALL XCOPYR(HEAP(HPSF(I)),XRNREF,HEAP(HPSF(I)),REFLCT)
               2
Argument #3 of `xcopyr' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f: In subroutine `xwrit2':
xrmani.f:801:
          SUBROUTINE XCOPY(ARRAY,REFLCT,CTEMP,REFLCT2)
                     1
xrmani.f:2642: (continued):
          CALL XCOPY(CTEMP,1,HEAP(HPSF(I)),REFLCT)
               2
Argument #3 of `xcopy' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f:817:
          SUBROUTINE XCOPYR(ARRAY,REFLCT,TEMP,REFLCT2)
                     1
xrmani.f:2646: (continued):
          CALL XCOPYR(TEMP,1,HEAP(HPSF(I)),REFLCT)
               2
Argument #3 of `xcopyr' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f:801:
          SUBROUTINE XCOPY(ARRAY,REFLCT,CTEMP,REFLCT2)
                     1
xrmani.f:2707: (continued):
          CALL XCOPY(CTEMP,1,HEAP(HPSF(IOBJ(I))),REFLCT)
               2
Argument #3 of `xcopy' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
xrmani.f:817:
          SUBROUTINE XCOPYR(ARRAY,REFLCT,TEMP,REFLCT2)
                     1
xrmani.f:2724: (continued):
          CALL XCOPYR(TEMP,1,HEAP(HPSF(IOBJ(I))),REFLCT)
               2
Argument #3 of `xcopyr' is one type at (2) but is some other type at
(1) [info -f g77 M GLOBALS]
mv: can't stat source xrmani.o

Dear all,
  I am installing cns1.1 under Red Hat Enterprise Linux 3 on a Dell Precision
worstation 470 (dual Xeon). I followed the installation notes described in
message 1334 just changing the compilers (using intel_fc_80 and intel_cc_80
instead of intel/fce/9.0 and intel/cce/9.0) (see below).
the 64bit version was compiled like
1) create a x86_64 directory under linux
2) copy the contents of the intel-i686-linux into x86_64
3) modify the getarch script to return x86_64 instead of unknown-something
4) source /opt/intel/fce/9.0/bin/ifortvars.csh
5) source /opt/intel/cce/9.0/bin/iccvars.csh
6) use the following x86_64/Makefile.header
# the -xP option could be used but then there might be a problem on opteron
F77 = ifort
F77STD =
F77OPT = -O -xW -vec_report0 -i8
F77FLAGS = $(F77STD) $(F77OPT) $(EXT_F77FLAGS) $(F77BUG)

# C options
CC = icc
CCFLAGS = -O -DINTEGER='long int' -DCNS_ARCH_TYPE_$(CNS_ARCH_TYPE)
$(EXT_CCFLAGS)

# link options
LD = ifort
LDFLAGS = -i-static -xW

# utility programs
compile-utils:
@ cd $(CNS_INST)/utils; \
make utils F77="$(F77)" CC="$(CC)" \
F77FLAGS="-w -O" CCFLAGS="-O" \
F77LINK="-i-static" CCLINK="-lm"

then make g77install.
The C and Fortran compiler passed test and the compilation went fine as well
as as linking and the creation of an executable file.
However, when i run cns_solve i still got the error:
---------------------------------------------------------
%ALLHP error encountered: out of INTEGER range
(CNS is in mode: SET ABORT=NORMal END)
WARNING: program encountered a fatal error.
However, in interactive mode, program execution
will continue. Proceed at your own risk.
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 160000 bytes
Maximum dynamic memory overhead: 12 bytes
Program started at: on
Program stopped at: 14:36:07 on 19-Sep-05
CPU time used: 0.0000 seconds
============================================================

Anyone has an idea how to compile cns1.1 with our machine?
Thanks,
Nadège



Nadège Jamin
DSV/DBJC/SBFM et URA CNRS 2096
C.E. Saclay
Bat 532
91191 Gif sur Yvette Cedex
FRANCE

Phone 33-1 69 08 25 46
Fax 33 -1 69 08 81 39

i am now using fortan95 by Lahey, and experience problems linking the
file now

Dear Colleague,

We are pleased to announce our first call for proposals for beam time at
sector 23 of the APS.  Beamline 23ID-D, currently operational, is the
first of two undulator beamlines being constructed at GM/CA CAT, funded
by NIGMS and NCI of the U.S. NIH.

Proposals for beamtime should be submitted to the APS on-line proposal
system (see
http://www.aps.anl.gov/Users/Scientific_Access/General_User/index.html).
For time at GM/CA CAT, indicate 23ID-D as your first choice.

For administrative questions about GM/CA CAT, please contact Sheila
Rossi at srossi@... or (630)252-0662.  For current beamline
capabilities and updates, please visit
http://www.gmca.aps.anl.gov/user_program/Envelope/Idin.html

With best regards,
GM/CA staff.

Oops, please use the site
http://www.gmca.aps.anl.gov/user_program/EnvelopeIDin.html
For current beamline capabilities.
Sorry for any confusion.
Nukri


Ruslan Sanishvili (Nukri), Ph.D.

GM/CA-CAT, Bld. 436, D007
Biosciences Division, ANL
9700 S. Cass Ave.
Argonne, IL 60439

Tel: (630)252-0665
Fax: (630)252-0667
rsanishvili@...




-----Original Message-----
From: cnsbb@yahoogroups.com [mailto:cnsbb@yahoogroups.com] On Behalf Of
Sanishvili, Ruslan
Sent: Monday, October 10, 2005 4:41 PM
To: cnsbb@yahoogroups.com
Subject: [cnsbb] New PX beamline at APS

Dear Colleague,

We are pleased to announce our first call for proposals for beam time at
sector 23 of the APS.  Beamline 23ID-D, currently operational, is the
first of two undulator beamlines being constructed at GM/CA CAT, funded
by NIGMS and NCI of the U.S. NIH.

Proposals for beamtime should be submitted to the APS on-line proposal
system (see
http://www.aps.anl.gov/Users/Scientific_Access/General_User/index.html).
For time at GM/CA CAT, indicate 23ID-D as your first choice.

For administrative questions about GM/CA CAT, please contact Sheila
Rossi at srossi@... or (630)252-0662.  For current beamline
capabilities and updates, please visit
http://www.gmca.aps.anl.gov/user_program/Envelope/Idin.html

With best regards,
GM/CA staff.



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Dear All,

I met a problem when using Xplor PARArestraints xpcs module.

The script I use is based on the sampe input file downloaded from
www.postgenomicnmr.net, and revised as the following (see the bottom).
Briefly speaking, I generate the psf file for the protein plus ANI, with or
without the file for cobalt.

The problem is that the the cobalt tensor parameters $chiax and $chirh should
converge after several iterations (50 structures x 5 interations), but my
results show that they don't. Something like this:
saCONV_1_10.pdb:REMARK xpcs coefficient.: 9480.79 -6012.09
saCONV_1_11.pdb:REMARK xpcs coefficient.: 13515 -7734.1
saCONV_1_12.pdb:REMARK xpcs coefficient.: 9331.34 -6128.62
saCONV_1_13.pdb:REMARK xpcs coefficient.: 26393.5 -17358.1
.....
saCONV_2_11.pdb:REMARK xpcs coefficient.: 2.389801E+06 -1.571383E+06
saCONV_2_12.pdb:REMARK xpcs coefficient.: 173188 -111816
saCONV_2_13.pdb:REMARK xpcs coefficient.: 2.043607E+06 -1.352478E+06
saCONV_2_14.pdb:REMARK xpcs coefficient.: 6.396403E+06 -4.250398E+06
....
saCONV_3_10.pdb:REMARK xpcs coefficient.: 2210.77 -1206.25
saCONV_3_11.pdb:REMARK xpcs coefficient.: 1200.21 -324.95
saCONV_3_12.pdb:REMARK xpcs coefficient.: 1338.83 -793.126
saCONV_3_14.pdb:REMARK xpcs coefficient.: 1928.36 -508.823
....
saCONV_4_10.pdb:REMARK xpcs coefficient.: 916869 -602598
saCONV_4_11.pdb:REMARK xpcs coefficient.: 56444.6 -36374.3
saCONV_4_12.pdb:REMARK xpcs coefficient.: 36311.4 -20406.6
saCONV_4_13.pdb:REMARK xpcs coefficient.: 80822.9 -50343.3
....
saCONV_5_10.pdb:REMARK xpcs coefficient.: 1914.45 -802.257
saCONV_5_11.pdb:REMARK xpcs coefficient.: 1782.43 -935.74
saCONV_5_12.pdb:REMARK xpcs coefficient.: 949.112 -348.363
saCONV_5_13.pdb:REMARK xpcs coefficient.: 2037.34 -923.342
....
In some interations (saCONV_2_*.pdb, saCONV_4_*.pdb, etc), the absolute value
of $chiax and $chirh goes extremely large, but the output structures seem ok,
with normal energy terms and coordinates. In other interations
(saCONV_3_*.pdb, saCONV_5_*.pdb, etc), their range look normal, but, in such
iterations, there is no noe or xpcs violations, the enegy terms are very low
(overall energy ~10^-2, noe energy ~10^-2), and the structure calculation
obviously fails, since in the output pdb file, the atom coordinates are like:
ATOM      1  CA  ALA     1      -5.594   3.278   2.303  1.00  0.00      PDZ2
ATOM      2  HA  ALA     1     604.428 354.780 285.185  1.00  0.00      PDZ2
ATOM      3  CB  ALA     1      -7.131   2.805   1.318  1.00  0.00      PDZ2
ATOM      4  HB1 ALA     1     603.126 354.814 283.656  1.00  0.00      PDZ2
ATOM      5  HB2 ALA     1     601.765 353.323 285.126  1.00  0.00      PDZ2
ATOM      6  HB3 ALA     1     604.055 353.268 284.413  1.00  0.00      PDZ2
ATOM      7  C   ALA     1      -4.757   1.565   3.007  1.00  0.00      PDZ2
ATOM      8  O   ALA     1      -4.389   1.031   3.855  1.00  0.00      PDZ2
ATOM      9  N   ALA     1      -4.755   4.462   2.234  1.00  0.00      PDZ2
ATOM     10  HT1 ALA     1      -4.673   4.437   3.255  1.00  0.00      PDZ2
ATOM     11  HT2 ALA     1      -5.589   4.552   1.511  1.00  0.00      PDZ2
ATOM     12  HT3 ALA     1      -4.115   4.075   1.669  1.00  0.00      PDZ2
ATOM     13  N   GLU     2      -4.614   0.980   1.619  1.00  0.00      PDZ2
ATOM     14  HN  GLU     2     606.603 356.257 286.373  1.00  0.00      PDZ2
ATOM     15  CA  GLU     2      -3.806   0.003   1.743  1.00  0.00      PDZ2
.............

I tried several ways of calculation, with or without the cobalt psf and pdb
file, with or without the initial setting of xpcs coefficient, and with
different force constant from 2 to 5. However, it makes no difference. I
don't know whether the problem lies in the xplor scripts I used, or the
paramagnetic restraints table, or the molecular topology file, or
something..... Could anyone give me some advice and help? Thanks a lot.

The xplor script I used:
===================================
evaluate ($init_t = 1000)
evaluate ($high_steps = 12000)
evaluate ($cool_steps = 6000)

parameter
  @TOPPAR:protein-1.0.par
  @TOPPAR:axis-1.0.par
end

topology
  @TOPPAR:protein-1.0.top
  @TOPPAR:top_axis.pro
  MASS   CO   58.9332  ! Cobalt
  residue COB
    atom CO type=CO charge=2.0 end
  end
end

structure @./reference/pdz2_ani_template.psf end
structure @./reference/cobalt.psf end
coordinates @./reference/pdz2_ani_template.pdb
coordinates @./reference/cobalt.pdb

noe
  nres=5000
  class tensor
  @./restraints/tensors.tbl
  class 1
  @./restraints/pdz2_nnoe.tbl
end

restraints dihedral
    reset
    @./restraints/pdz2_dihed.tbl
end

flags exclude * include bonds angle impr vdw noe xpcs end

vector do (fbeta=10) (all)
vector do (mass=100) (all)

noe
  ceiling=1000
  averaging  * cent
  potential  * soft
  scale * 50.
  sqoffset   * 0.0
  sqconstant * 1.0
  sqexponent * 2
  soexponent * 1
  asymptote  * 0.1
  rswitch    * 0.5
end

xpcs
  nres=2000
  class cobalt
  force 2
  coeff 1600 -500
  @./restraints/pcstable_pdz2_3.tbl
end

parameter
  nbonds
   repel=1.
   rexp=2 irexp=2 rcon=1.
   nbxmod=3
   wmin=0.01
   cutnb=4.5 ctonnb=2.99 ctofnb=3.
   tolerance=0.5
  end
end

set abort off end

evaluate ($end_count=50)                      { 50 structures per step }

coor copy end

evaluate ($count1 = 0)
while ($count1 < 5 ) loop media              { 10 steps }
evaluate ($count1=$count1+1)
   evaluate ($count = 0)
   while ($count < $end_count ) loop main
   evaluate ($count=$count+1)
   coor swap end
   coor copy end
   noe
     potential * soft
   end

   {* ============================================ Initial minimization.*}
  .............
   {* ======================================= High-temperature dynamics.*}
.............
   {* ============= Tilt the asymptote and increase weights on geometry.*}
.............
   {* ================================================  Cool the system.*}
.............
   {===============================================>} {*Abort condition.*}
............
   {* ============================================== Final minimization.*}
............
     xpcs
      foff
      son
      evaluate
($filename="./pdz2/test16/1pse"+encode($count1)+"_"+encode($count))
      save $filename
      frun 1
      soff
     end

   {* ================================ Write out the final structure(s).*}
...........................
   end loop main

  xpcs
   fmed 10 1
   class cobalt
   coeff $chiax $chirh
   fmed 1 0
  end

end loop media

xpcs
  erron 10 35
  frun 1
end

stop
====================================


Thanks,
Victor

Hi all,

I'm running CNS on Redhat 9.  I have no problem running any programs,
but certain files seem to be made in a bad format that cannot be read
by other programs.  When making a map file and subsequently trying to
load the map into O, I get this error:

fmt: read unexpected character
apparent state: unit 2 named composite_omit_map.map
last format: (6e12.5)
lately reading sequential formatted external IO
Abort

Similarly, ccp4 and mapman are unable to read this file.  Does anyone
have any suggestions?  I really would appreciate any help!

Thanks,
Stephanie

Dear colleagures,

I used "model_map.inp" in CNS to calculate 2Fo-Fc map,
but, to avoid the model bias, I just learned I should
use Fo-Fc map as well. But, I searched for the script
again and again and couldn't find it. Could anybody
kindly tell me which script in CNS I should use to
calculate Fo-Fc map?

I am new to protein crytallography and none of people
around me knows crystallography. Please help me!

Thank you very much!

ES



__________________________________
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In model_map_2-1.inp under the section map generation parameters:


{==================== map generation parameters ======================}

{* maps are calculated u*Fo - v*Fc *}
{* eg. 2fo-fc map -> u=2 and v=1 or
         fo-fc map -> u=1 and v=1 *}

{* specify u *}
{===>} u=2;

{* specify v *}
{===>} v=1;



change the u=2 to u=1 as is suggested and save the output file as
model_map_1-1.inp

run both programs seperately and you will have a 2fo-fc and a fo-fc
output as a .map file

Lorien


CNS ER wrote:
>
> Dear colleagures,
>
> I used "model_map.inp" in CNS to calculate 2Fo-Fc map,
> but, to avoid the model bias, I just learned I should
> use Fo-Fc map as well. But, I searched for the script
> again and again and couldn't find it. Could anybody
> kindly tell me which script in CNS I should use to
> calculate Fo-Fc map?
>
> I am new to protein crytallography and none of people
> around me knows crystallography. Please help me!
>
> Thank you very much!
>
> ES
>
>
> __________________________________
> Start your day with Yahoo! - Make it your home page!
> http://www.yahoo.com/r/hs
>
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
>
> Yahoo! Groups Links
>
>
>
>

--
Lorien Parker
Ph.D. Student
Biota Structural Biology Laboratory
St. Vincent's Institute
9 Princes St
Fitzroy, VIC 3065
Australia
Ph: +61 03 92882480

PLEASE NOTE NEW EMAIL ADDRESS: lparker@...

Hi:

It's the same script - you just have to change the u/v coefficients to
1 for the Fo-Fc map (see below)


{==================== map generation parameters ======================}

{* maps are calculated u*Fo - v*Fc *}
{* eg. 2fo-fc map -> u=2 and v=1 or
          fo-fc map -> u=1 and v=1 *}

{* specify u *}
{===>} u=1;

{* specify v *}
{===>} v=1;

Hope this helps,
Alexandra



On Thursday, October 27, 2005, at 01:00 AM, CNS ER wrote:

> Dear colleagures,
>
> I used "model_map.inp" in CNS to calculate 2Fo-Fc map,
> but, to avoid the model bias, I just learned I should
> use Fo-Fc map as well. But, I searched for the script
> again and again and couldn't find it. Could anybody
> kindly tell me which script in CNS I should use to
> calculate Fo-Fc map?
>
> I am new to protein crytallography and none of people
> around me knows crystallography. Please help me!
>
> Thank you very much!
>
> ES
>
>
>
> __________________________________
> Start your day with Yahoo! - Make it your home page!
> http://www.yahoo.com/r/hs
>
>
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
>
> Yahoo! Groups Links
>
>
>
>
>
>
>

To whom it may concern,

Has anyone had any problems finding peaks using model_map.inp or water_pick.inp
in
CNS
1.1.  Looking at the log file, it seems like there's a problem with the peak
picking
algorithm
used by CNS.  The scripts fail to pick positive and negative peaks.  In the case
of the
model_map.inp script, all map files are generated but the negative and postive
peak files
are not.  Nothing is generated when I run the the water_pick.inp script. 
Inspection of the
fo-fc
electron density map clearly show strong (~3-6 sigma) positive and negative
peaks.  I have
no idea what the problem is.  What is even more confusing is that I can ftp the
input files
to another computer which is running CNS 1.0 (I need to change checkversion from
1.1 to
1.0) and the scripts run fine with no errors.  I believe CNS 1.1 is setup
(envrioment
varibables, etc.) correctly because all of the other input files tried so far
work correctly.
Does anyone have any ideas?  A bit of the log file of water_pick.inp is shown
below:

                ( &atom_select and not segid PEAK) saround &hmax ) )
  SELRPN:      0 atoms have been selected out of   5490
  DELETE>   end
  SCRATC-warning: XRAY SCATter database erased.
  Status of internal molecular topology database:
  -> NATOM=       5490(MAXA=       40000)  NBOND=       5499(MAXB=       40000)
  -> NTHETA=      7414(MAXT=       80000)  NGRP=         758(MAXGRP=     40000)
  -> NPHI=        3344(MAXP=       80000)  NIMPHI=      2347(MAXIMP=     40000)
  -> NNB=            0(MAXNB=      40000)
  CNSsolve>   delete sele=      ( segid PEAK and
  SELRPN>                 ( ( ( &atom_select and not segid PEAK ) saround &hmax )
and
  SELRPN>              not  ( ( ( &atom_select and not segid PEAK ) and
  SELRPN>                       ( name O* or name N* ) ) saround &hmax ) ) )
  SELRPN:      0 atoms have been selected out of   5490
  DELETE>   end
  SCRATC-warning: XRAY SCATter database erased.
  Status of internal molecular topology database:
  -> NATOM=       5490(MAXA=       40000)  NBOND=       5499(MAXB=       40000)
  -> NTHETA=      7414(MAXT=       80000)  NGRP=         758(MAXGRP=     40000)
  -> NPHI=        3344(MAXP=       80000)  NIMPHI=      2347(MAXIMP=     40000)
  -> NNB=            0(MAXNB=      40000)
  CNSsolve> end if
  CNSsolve>
  CNSsolve> parameter nbonds special_position=&special_dist end end
  CNSsolve>
  CNSsolve> if ( &peak_special = false ) then
  NEXTCD: condition evaluated as true
  CNSsolve>   xray
  XRAY>     @@CNS_XRAYLIB:scatter.lib
  ASSFIL: file
/usr/local/src/crystallography/cns_solve_1.1/libraries/xray/scatter.lib
opened.
  XRAY>! file libraries/xray/scatter.lib
  XRAY>! Atomic scattering factors without anomalous contribution
  XRAY>! Library for CNS
  XRAY>
  XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
  XRAY>
  XRAY>!BEWARE:
  XRAY>!(1) element Cf (Californium) has to be referred to as Cff
  XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
  XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
  XRAY>!(3) types of elements with ionic state (i.e., +/-) specifications have
  XRAY>!    to be put in double quotes in selection statements.
  XRAY>
  XRAY>set message ? end
  MESSage=NORM
  XRAY>evaluate ($message_old_sclib=$result)
  EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
  XRAY>set echo ? end
  ECHO=TRUE {ON}
  XRAY>evaluate ($echo_old_sclib=$result)
  EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
  XRAY>set echo=off message=off end
  Program version= 1.1 File version= 1.1
  XRAY>     special selection=( segid PEAK ) to=rmsd end
  SELRPN:      0 atoms have been selected out of   5490
  %XSPEcial-ERR: zero atoms selected.
  %XSPEcial error encountered: zero atoms selected.
    (CNS is in mode: SET ABORT=NORMal END)
  *****************************************************
  ABORT mode will terminate program execution.

Hi,
I have a student who has the following trouble running the
cross_rotation.inp script.
My data is partial twin according to detect_twinning.inp. Therefore,
I had run detwin_partial.inp on CNS.
And I have got a detwin_partial.hkl.
And I have run a cross_rotation.inp on CNS.
But I got a error message.

If anyone can suggest some trouble shooting tips that would be
greatly
appreciated.
Thanks in advance for any replies.

If you need further info please let me know.


It is error message.

XDECLARE: Object TEST_DET has been declared.
  REFLection> INDE    45    8    2 FOBS_DET=     3.069 SIGMA_DET=
3.330
  XSFAL: allocating space for real reciprocal space object.
  XSFAL: allocating space for real reciprocal space object.
  XSFAL: allocating space for integer reciprocal space object.
  XRRR2:    39180 new h,k,l indices have been added.
  XRAY>
  XRAY>   binresolution &low_res &high_res
  XRAY>   mapresolution &high_res
  XRAY>
  XRAY>   set echo=off end
  NEXTCD: condition evaluated as false
  Reciprocal space object FOBS does not exist.
  NEXTCD: condition evaluated as true


Sincerely yours

Kyoung Hoon, Kim

This is prviously posted by Mark A. White, hope this helps!

-------------------------

Hi,

The problem may be one which Joe Krahn found earlier,  memory allocation
under Linux.  Here is his fix for the problem, which was posted to the
CCP4 bulletin board.  You will need to recompile CNS after fixing the code.


**  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Many F77 programs access memory from C malloc() via
an out-of-bounds index to a HEAP array. It seems that
malloc() used to always generate a positive array index
in Linux (and presumably other OSes) but malloc() in
Fedora and Enterprise Linux most often gives a negative
array index.

This exposes a bug in CNS, as well as some of my own code.
It might affect other programs using C malloc() from F77.

The bug and fix in CNS is in xpeakpik.f, which results in
never getting any peaks picked:

*** 143,147 ****
         DONE=.FALSE.
   C
!       IF (MPACK.GT.0) THEN
   C
         IF (.NOT.ERR.AND.HPRRHO(IFROM).EQ.0) THEN
--- 143,147 ----
         DONE=.FALSE.
   C
!       IF (MPACK.NE.0) THEN
   C
         IF (.NOT.ERR.AND.HPRRHO(IFROM).EQ.0) THEN

The intent is to check if MPACK Heap memory is allocated,
i.e. if MPACK==NULL, which worked only if the MPACK was positive.

Joe Krahn


-----------------------------

Best Regards,

Mark

-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_
Mark A. White, Ph.D.                                Tel:
Sealy Center for Structural Biology                 (409) 747-4747
Dept. of Human Biological Chemistry & Genetics      Fax:
Basic Science Building, Room 660C                   (409) 747-4745
University of Texas Medical Branch                  email:
Galveston, TX 77555-0647              mailto://white@xray.utmb.edu
http://xray.utmb.edu                  http://xray.utmb.edu/~white
-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_-_

------------------------------

Tiancen Hu
Shanghai Institute of Materia Medica







>To whom it may concern,
>
>Has anyone had any problems finding peaks using model_map.inp or water_pick.inp
in
>CNS
>1.1.  Looking at the log file, it seems like there's a problem with the peak
picking
>algorithm
>used by CNS.  The scripts fail to pick positive and negative peaks.  In the
case of the
>model_map.inp script, all map files are generated but the negative and postive
peak files
>are not.  Nothing is generated when I run the the water_pick.inp script. 
Inspection of the
>fo-fc
>electron density map clearly show strong (~3-6 sigma) positive and negative
peaks.  I have
>no idea what the problem is.  What is even more confusing is that I can ftp the
input files
>to another computer which is running CNS 1.0 (I need to change checkversion
from 1.1 to
>1.0) and the scripts run fine with no errors.  I believe CNS 1.1 is setup
(envrioment
>varibables, etc.) correctly because all of the other input files tried so far
work correctly.
>Does anyone have any ideas?  A bit of the log file of water_pick.inp is shown
below:
>
>               ( &atom_select and not segid PEAK) saround &hmax ) )
> SELRPN:      0 atoms have been selected out of   5490
> DELETE>   end
> SCRATC-warning: XRAY SCATter database erased.
> Status of internal molecular topology database:
> -> NATOM=       5490(MAXA=       40000)  NBOND=       5499(MAXB=       40000)
> -> NTHETA=      7414(MAXT=       80000)  NGRP=         758(MAXGRP=     40000)
> -> NPHI=        3344(MAXP=       80000)  NIMPHI=      2347(MAXIMP=     40000)
> -> NNB=            0(MAXNB=      40000)
> CNSsolve>   delete sele=      ( segid PEAK and
> SELRPN>                 ( ( ( &atom_select and not segid PEAK ) saround &hmax
) and
> SELRPN>              not  ( ( ( &atom_select and not segid PEAK ) and
> SELRPN>                       ( name O* or name N* ) ) saround &hmax ) ) )
> SELRPN:      0 atoms have been selected out of   5490
> DELETE>   end
> SCRATC-warning: XRAY SCATter database erased.
> Status of internal molecular topology database:
> -> NATOM=       5490(MAXA=       40000)  NBOND=       5499(MAXB=       40000)
> -> NTHETA=      7414(MAXT=       80000)  NGRP=         758(MAXGRP=     40000)
> -> NPHI=        3344(MAXP=       80000)  NIMPHI=      2347(MAXIMP=     40000)
> -> NNB=            0(MAXNB=      40000)
> CNSsolve> end if
> CNSsolve>
> CNSsolve> parameter nbonds special_position=&special_dist end end
> CNSsolve>
> CNSsolve> if ( &peak_special = false ) then
> NEXTCD: condition evaluated as true
> CNSsolve>   xray
> XRAY>     @@CNS_XRAYLIB:scatter.lib
> ASSFIL: file
/usr/local/src/crystallography/cns_solve_1.1/libraries/xray/scatter.lib
>opened.
> XRAY>! file libraries/xray/scatter.lib
> XRAY>! Atomic scattering factors without anomalous contribution
> XRAY>! Library for CNS
> XRAY>
> XRAY>! Authors: Paul Adams, Joe Jaeger, and Axel T. Brunger
> XRAY>
> XRAY>!BEWARE:
> XRAY>!(1) element Cf (Californium) has to be referred to as Cff
> XRAY>!(2) element Sm (Samarium) has to be referred to as Smm
> XRAY>!(3) element Np (Neptunium) has to be referred to as Npp
> XRAY>!(3) types of elements with ionic state (i.e., +/-) specifications have
> XRAY>!    to be put in double quotes in selection statements.
> XRAY>
> XRAY>set message ? end
> MESSage=NORM
> XRAY>evaluate ($message_old_sclib=$result)
> EVALUATE: symbol $MESSAGE_OLD_SCLIB set to "NORM" (string)
> XRAY>set echo ? end
> ECHO=TRUE {ON}
> XRAY>evaluate ($echo_old_sclib=$result)
> EVALUATE: symbol $ECHO_OLD_SCLIB set to TRUE (logical)
> XRAY>set echo=off message=off end
> Program version= 1.1 File version= 1.1
> XRAY>     special selection=( segid PEAK ) to=rmsd end
> SELRPN:      0 atoms have been selected out of   5490
> %XSPEcial-ERR: zero atoms selected.
> %XSPEcial error encountered: zero atoms selected.
>   (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
>
>
>
>
>
>
>--------------------------------------------------------
>List information at http://groups.yahoo.com/group/cnsbb.
>Posting is only allowed for members of this list.
>
>
>Yahoo! Groups Links
>
>
>
>
>
>
>
>
>

Hi,

   I currently trying to simulate some proteins, and I would like to
parallize the CNS code (anneal.inp) to run on two or three processors.
Has anyone done this? Any help is appreciated!

Thanks,
Steve

The topology/parameter file combinations for ligands generated by XPLO2D have
the potential of pulling back the ligand into the original conformation from
which the parameters were derived from.  XPLO2D is not psychic about all the
intermal degrees of flexibility in your ligand.  This is probably mostly a
result of DIHEdral and sometimes IMPRoper lines in the topology file.  A simple
but brutal method would be to comment all of them out.  A more elegant method
would be to list the high energy geometric deviations before refinement, figure
out what DIHEdral terms they correspond to, and comment just those out.

(I knew how to do that in X-PLOR, I'm not sure how to do that in CNS, but there
must be a way).

Phil Jeffrey
Princeton University

----- Original Message -----
From: Zeqiang Ma <zqma@...>
Date: Wednesday, November 9, 2005 7:39 pm
Subject: [cnsbb] Ligand minimization
To: cnsbb@yahoogroups.com
Cc: zqma@...

> Dear all,
>
>
>
> I am a new user of CNS and here I have a question about ligand
> minimization.I downloaded ligand coordinate, topology and parameter
> files from Hic-Up and
> put them in my protein structure by Coot. The ligand electron
> density is
> pretty clear and there are no error messages in refinement steps.
> But the
> problem is, every time when I modified the ligand in Coot, it would
> alwayschange back to the same structure as original coordinate file
> after running
> minimize.inp. It looks like the ligand coordinate won't try to fit the
> electron density.  I guess I missed some points for using CNS. If
> anyone has
> any idea about it, please let me know. I appreciate any suggestion
> aboutligand refinement.
>
>
>
> Thanks.
>
>
>
> Zeqiang
>
>
>
>
>
> PS:
>
> Here are the copies of topology and parameter files:
>
>
>
> Remarks nlp_xplor_top.txt
>
> Remarks Created by XPLO2D V. 041005/3.3.1 at Tue Jan 25 23:36:25
> 2005 for A.
> Nonymous
>
> Remarks Auto-generated by XPLO2D from file nlp_msd.pdb
>
> Remarks You *MUST* check/edit MASSes and CHARges !!!
>
> Remarks Check DONOrs and ACCEptors
>
> Remarks Verify IMPRopers yourself
>
> Remarks DIHEdrals which are not flat are commented out
>
>
>
> set echo=false end
>
>
>
> { Note: edit masses if necessary }
>
> MASS N_1    15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
>
> MASS C_2    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
>
> MASS C_3    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
> MASS C_4    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
> MASS C_5    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
> MASS C_6    15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs)
>
> MASS P_7    30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs)
>
> MASS O_8    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
> MASS O_9    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
> MASS O_10   17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
>
>
> autogenerate angles=true end
>
>
>
> RESIdue NLP
>
>
>
> { Note: electrostatics should normally not be used in }
>
> { crystallographic refinement since it can produce }
>
> { artefacts. For this reason, all charges are set to }
>
> { zero by default. Edit them if necessary }
>
> GROUp
>
> ATOM  N    TYPE N_1   CHARge  0.0  END ! Nr of Hs =  1
>
> ATOM  CA   TYPE C_2   CHARge  0.0  END ! Nr of Hs =  1
>
> ATOM  CB   TYPE C_3   CHARge  0.0  END ! Nr of Hs =  2
>
> ATOM  CG   TYPE C_4   CHARge  0.0  END ! Nr of Hs =  2
>
> ATOM  CD   TYPE C_5   CHARge  0.0  END ! Nr of Hs =  2
>
> ATOM  CE   TYPE C_6   CHARge  0.0  END ! Nr of Hs =  3
>
> ATOM  P    TYPE P_7   CHARge  0.0  END ! Nr of Hs =  0
>
> ATOM  O1   TYPE O_8   CHARge  0.0  END ! Nr of Hs =  1
>
> ATOM  O2   TYPE O_9   CHARge  0.0  END ! Nr of Hs =  1
>
> ATOM  O3   TYPE O_10  CHARge  0.0  END ! Nr of Hs =  1
>
>
>
> BOND  N    CA       BOND  CA   CB       BOND  CA   P        BOND
> CB   CG
>
> BOND  CG   CD       BOND  CD   CE       BOND  P    O1       BOND
> P    O2
>
> BOND  P    O3
>
>
>
> { Note: edit these DIHEdrals if necessary }
>
>  DIHEdral  N    CA   CB   CG  ! flat ? (180 degrees = trans)   179.96
>
> ! DIHEdral  P    CA   CB   CG  ! flexible dihedral ???    60.00
>
> ! DIHEdral  N    CA   P    O1  ! flexible dihedral ???   -59.98
>
> ! DIHEdral  N    CA   P    O2  ! flexible dihedral ???    60.00
>
>  DIHEdral  N    CA   P    O3  ! flat ? (180 degrees = trans)   180.00
>
> ! DIHEdral  CB   CA   P    O1  ! flexible dihedral ???    59.99
>
>  DIHEdral  CB   CA   P    O2  ! flat ? (180 degrees = trans)   179.97
>
> ! DIHEdral  CB   CA   P    O3  ! flexible dihedral ???   -60.03
>
>  DIHEdral  CA   CB   CG   CD  ! flat ? (180 degrees = trans)   180.01
>
>  DIHEdral  CB   CG   CD   CE  ! flat ? (180 degrees = trans)   180.01
>
>
>
> { Note: edit these IMPRopers if necessary }
>
> IMPRoper  CA   N    CB   P   ! chirality or flatness improper   -
> 37.82
> IMPRoper  P    CA   O1   O2  ! chirality or flatness improper   -
> 35.15
>
>
> { Note: edit any DONOrs and ACCEptors if necessary }
>
> ! DONOr H?1  N
>
> ACCEptor  O1   P
>
> ACCEptor  O2   P
>
> ACCEptor  O3   P
>
>
>
> END { RESIdue NLP }
>
>
>
>
>
>
>
>
>
> Remarks nlp_xplor_par.txt
>
> Remarks Created by XPLO2D V. 041005/3.3.1 at Tue Jan 25 23:36:25
> 2005 for A.
> Nonymous
>
> Remarks Auto-generated by XPLO2D from file nlp_msd.pdb
>
> Remarks Parameters for residue type NLP
>
>
>
> set echo=false end
>
>
>
> { Note: edit if necessary }
>
> BOND N_1  C_2    1000.0  1.469 ! Nobs =    1
>
> BOND C_2  C_3    1000.0  1.528 ! Nobs =    1
>
> BOND C_2  P_7    1000.0  1.822 ! Nobs =    1
>
> BOND C_3  C_4    1000.0  1.530 ! Nobs =    1
>
> BOND C_4  C_5    1000.0  1.529 ! Nobs =    1
>
> BOND C_5  C_6    1000.0  1.529 ! Nobs =    1
>
> BOND P_7  O_8    1000.0  1.480 ! Nobs =    1
>
> BOND P_7  O_9    1000.0  1.610 ! Nobs =    1
>
> BOND P_7  O_10   1000.0  1.610 ! Nobs =    1
>
>
>
> { Note: edit if necessary }
>
> ANGLe N_1  C_2  C_3     500.0   109.45 ! Nobs =    1
>
> ANGLe N_1  C_2  P_7     500.0   109.43 ! Nobs =    1
>
> ANGLe C_3  C_2  P_7     500.0   109.51 ! Nobs =    1
>
> ANGLe C_2  C_3  C_4     500.0   109.48 ! Nobs =    1
>
> ANGLe C_3  C_4  C_5     500.0   109.52 ! Nobs =    1
>
> ANGLe C_4  C_5  C_6     500.0   109.51 ! Nobs =    1
>
> ANGLe C_2  P_7  O_8     500.0   109.49 ! Nobs =    1
>
> ANGLe C_2  P_7  O_9     500.0   109.48 ! Nobs =    1
>
> ANGLe C_2  P_7  O_10    500.0   109.46 ! Nobs =    1
>
> ANGLe O_8  P_7  O_9     500.0   109.44 ! Nobs =    1
>
> ANGLe O_8  P_7  O_10    500.0   109.48 ! Nobs =    1
>
> ANGLe O_9  P_7  O_10    500.0   109.47 ! Nobs =    1
>
>
>
> { Note: edit if necessary }
>
> DIHEdral N_1  C_2  C_3  C_4     750.0 0   180.00 ! Nobs =    1 ...
> Value =
> 179.96
>
> DIHEdral P_7  C_2  C_3  C_4     750.0 0    60.00 ! Nobs =    1 ...
> Value =
> 60.00
>
> DIHEdral N_1  C_2  P_7  O_8     750.0 0   -60.00 ! Nobs =    1 ...
> Value =
> -59.98
>
> DIHEdral N_1  C_2  P_7  O_9     750.0 0    60.00 ! Nobs =    1 ...
> Value =
> 60.00
>
> DIHEdral N_1  C_2  P_7  O_10    750.0 0   180.00 ! Nobs =    1 ...
> Value =
> 180.00
>
> DIHEdral C_3  C_2  P_7  O_8     750.0 0    60.00 ! Nobs =    1 ...
> Value =
> 59.99
>
> DIHEdral C_3  C_2  P_7  O_9     750.0 0   180.00 ! Nobs =    1 ...
> Value =
> 179.97
>
> DIHEdral C_3  C_2  P_7  O_10    750.0 0   -60.00 ! Nobs =    1 ...
> Value =
> -60.03
>
> DIHEdral C_2  C_3  C_4  C_5     750.0 0   180.00 ! Nobs =    1 ...
> Value =
> -179.99
>
> DIHEdral C_3  C_4  C_5  C_6     750.0 0   180.00 ! Nobs =    1 ...
> Value =
> -179.99
>
>
>
> { Note: edit if necessary }
>
> IMPRoper C_2  N_1  C_3  P_7     750.0 0  -35.000 ! Nobs =    1 ...
> Value =
> -37.817
>
> IMPRoper P_7  C_2  O_8  O_9     750.0 0  -35.000 ! Nobs =    1 ...
> Value =
> -35.155
>
>
>
> { Note: edit if necessary }
>
> NONBonded N_1  0.2384  2.8509    0.2384  2.8509 ! assuming Nitrogen
>
> NONBonded C_2  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
> NONBonded C_3  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
> NONBonded C_4  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
> NONBonded C_5  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
> NONBonded C_6  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
> NONBonded P_7  0.5849  3.3854    0.5849  3.3854 ! assuming
> Phosphorous
> NONBonded O_8  0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
> NONBonded O_9  0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
> NONBonded O_10 0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
>
>
> set echo=true end
>
>
>
>
>
>
>
>
>
>

Hi Zeqiang

Try to use PRODRG - this provides "ideal" parameters for your molecule, in
terms of bonds, angles etc. etc., not the ones that are in the PDB
file, which is what HICUP does. I strongly recommend that, rather than
inputting your PDB coordinates, you draw your ligand  with the JME editor
on the PRODRG server site and then use the coordinates and the CNS
topology/parameters that come out of that. Note that PRODRG also writes
out a REFMAC library file - if you read this into coot and then just click
on Real Space Refine zone with an approximately positioned ligand it will
fit it automatically!

Daan

On Wed, 9 Nov 2005, Zeqiang Ma wrote:

> Dear all,
>
>
>
> I am a new user of CNS and here I have a question about ligand minimization.
> I downloaded ligand coordinate, topology and parameter files from Hic-Up and
> put them in my protein structure by Coot. The ligand electron density is
> pretty clear and there are no error messages in refinement steps. But the
> problem is, every time when I modified the ligand in Coot, it would always
> change back to the same structure as original coordinate file after running
> minimize.inp. It looks like the ligand coordinate won't try to fit the
> electron density.  I guess I missed some points for using CNS. If anyone has
> any idea about it, please let me know. I appreciate any suggestion about
> ligand refinement.
>
>
>
> Thanks.
>
>
>
> Zeqiang
>
>
>
>
>
> PS:
>
> Here are the copies of topology and parameter files:
>
>
>
> Remarks nlp_xplor_top.txt
>
> Remarks Created by XPLO2D V. 041005/3.3.1 at Tue Jan 25 23:36:25 2005 for A.
> Nonymous
>
> Remarks Auto-generated by XPLO2D from file nlp_msd.pdb
>
> Remarks You *MUST* check/edit MASSes and CHARges !!!
>
> Remarks Check DONOrs and ACCEptors
>
> Remarks Verify IMPRopers yourself
>
> Remarks DIHEdrals which are not flat are commented out
>
>
>
>  set echo=false end
>
>
>
>  { Note: edit masses if necessary }
>
>  MASS N_1    15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs)
>
>  MASS C_2    13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs)
>
>  MASS C_3    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
>  MASS C_4    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
>  MASS C_5    14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs)
>
>  MASS C_6    15.03500 ! assuming C -> 12.01100 + 1.008 * 3 (Hs)
>
>  MASS P_7    30.97400 ! assuming P -> 30.97400 + 1.008 * 0 (Hs)
>
>  MASS O_8    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
>  MASS O_9    17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
>  MASS O_10   17.00700 ! assuming O -> 15.99900 + 1.008 * 1 (Hs)
>
>
>
>  autogenerate angles=true end
>
>
>
> RESIdue NLP
>
>
>
>  { Note: electrostatics should normally not be used in }
>
>  { crystallographic refinement since it can produce }
>
>  { artefacts. For this reason, all charges are set to }
>
>  { zero by default. Edit them if necessary }
>
> GROUp
>
>  ATOM  N    TYPE N_1   CHARge  0.0  END ! Nr of Hs =  1
>
>  ATOM  CA   TYPE C_2   CHARge  0.0  END ! Nr of Hs =  1
>
>  ATOM  CB   TYPE C_3   CHARge  0.0  END ! Nr of Hs =  2
>
>  ATOM  CG   TYPE C_4   CHARge  0.0  END ! Nr of Hs =  2
>
>  ATOM  CD   TYPE C_5   CHARge  0.0  END ! Nr of Hs =  2
>
>  ATOM  CE   TYPE C_6   CHARge  0.0  END ! Nr of Hs =  3
>
>  ATOM  P    TYPE P_7   CHARge  0.0  END ! Nr of Hs =  0
>
>  ATOM  O1   TYPE O_8   CHARge  0.0  END ! Nr of Hs =  1
>
>  ATOM  O2   TYPE O_9   CHARge  0.0  END ! Nr of Hs =  1
>
>  ATOM  O3   TYPE O_10  CHARge  0.0  END ! Nr of Hs =  1
>
>
>
>  BOND  N    CA       BOND  CA   CB       BOND  CA   P        BOND  CB   CG
>
>  BOND  CG   CD       BOND  CD   CE       BOND  P    O1       BOND  P    O2
>
>  BOND  P    O3
>
>
>
>  { Note: edit these DIHEdrals if necessary }
>
>   DIHEdral  N    CA   CB   CG  ! flat ? (180 degrees = trans)   179.96
>
> ! DIHEdral  P    CA   CB   CG  ! flexible dihedral ???    60.00
>
> ! DIHEdral  N    CA   P    O1  ! flexible dihedral ???   -59.98
>
> ! DIHEdral  N    CA   P    O2  ! flexible dihedral ???    60.00
>
>   DIHEdral  N    CA   P    O3  ! flat ? (180 degrees = trans)   180.00
>
> ! DIHEdral  CB   CA   P    O1  ! flexible dihedral ???    59.99
>
>   DIHEdral  CB   CA   P    O2  ! flat ? (180 degrees = trans)   179.97
>
> ! DIHEdral  CB   CA   P    O3  ! flexible dihedral ???   -60.03
>
>   DIHEdral  CA   CB   CG   CD  ! flat ? (180 degrees = trans)   180.01
>
>   DIHEdral  CB   CG   CD   CE  ! flat ? (180 degrees = trans)   180.01
>
>
>
>  { Note: edit these IMPRopers if necessary }
>
>  IMPRoper  CA   N    CB   P   ! chirality or flatness improper   -37.82
>
>  IMPRoper  P    CA   O1   O2  ! chirality or flatness improper   -35.15
>
>
>
>  { Note: edit any DONOrs and ACCEptors if necessary }
>
> ! DONOr H?1  N
>
>  ACCEptor  O1   P
>
>  ACCEptor  O2   P
>
>  ACCEptor  O3   P
>
>
>
> END { RESIdue NLP }
>
>
>
>
>
>
>
>
>
> Remarks nlp_xplor_par.txt
>
> Remarks Created by XPLO2D V. 041005/3.3.1 at Tue Jan 25 23:36:25 2005 for A.
> Nonymous
>
> Remarks Auto-generated by XPLO2D from file nlp_msd.pdb
>
> Remarks Parameters for residue type NLP
>
>
>
>  set echo=false end
>
>
>
>  { Note: edit if necessary }
>
>  BOND N_1  C_2    1000.0  1.469 ! Nobs =    1
>
>  BOND C_2  C_3    1000.0  1.528 ! Nobs =    1
>
>  BOND C_2  P_7    1000.0  1.822 ! Nobs =    1
>
>  BOND C_3  C_4    1000.0  1.530 ! Nobs =    1
>
>  BOND C_4  C_5    1000.0  1.529 ! Nobs =    1
>
>  BOND C_5  C_6    1000.0  1.529 ! Nobs =    1
>
>  BOND P_7  O_8    1000.0  1.480 ! Nobs =    1
>
>  BOND P_7  O_9    1000.0  1.610 ! Nobs =    1
>
>  BOND P_7  O_10   1000.0  1.610 ! Nobs =    1
>
>
>
>  { Note: edit if necessary }
>
>  ANGLe N_1  C_2  C_3     500.0   109.45 ! Nobs =    1
>
>  ANGLe N_1  C_2  P_7     500.0   109.43 ! Nobs =    1
>
>  ANGLe C_3  C_2  P_7     500.0   109.51 ! Nobs =    1
>
>  ANGLe C_2  C_3  C_4     500.0   109.48 ! Nobs =    1
>
>  ANGLe C_3  C_4  C_5     500.0   109.52 ! Nobs =    1
>
>  ANGLe C_4  C_5  C_6     500.0   109.51 ! Nobs =    1
>
>  ANGLe C_2  P_7  O_8     500.0   109.49 ! Nobs =    1
>
>  ANGLe C_2  P_7  O_9     500.0   109.48 ! Nobs =    1
>
>  ANGLe C_2  P_7  O_10    500.0   109.46 ! Nobs =    1
>
>  ANGLe O_8  P_7  O_9     500.0   109.44 ! Nobs =    1
>
>  ANGLe O_8  P_7  O_10    500.0   109.48 ! Nobs =    1
>
>  ANGLe O_9  P_7  O_10    500.0   109.47 ! Nobs =    1
>
>
>
>  { Note: edit if necessary }
>
>  DIHEdral N_1  C_2  C_3  C_4     750.0 0   180.00 ! Nobs =    1 ... Value =
> 179.96
>
>  DIHEdral P_7  C_2  C_3  C_4     750.0 0    60.00 ! Nobs =    1 ... Value =
> 60.00
>
>  DIHEdral N_1  C_2  P_7  O_8     750.0 0   -60.00 ! Nobs =    1 ... Value =
> -59.98
>
>  DIHEdral N_1  C_2  P_7  O_9     750.0 0    60.00 ! Nobs =    1 ... Value =
> 60.00
>
>  DIHEdral N_1  C_2  P_7  O_10    750.0 0   180.00 ! Nobs =    1 ... Value =
> 180.00
>
>  DIHEdral C_3  C_2  P_7  O_8     750.0 0    60.00 ! Nobs =    1 ... Value =
> 59.99
>
>  DIHEdral C_3  C_2  P_7  O_9     750.0 0   180.00 ! Nobs =    1 ... Value =
> 179.97
>
>  DIHEdral C_3  C_2  P_7  O_10    750.0 0   -60.00 ! Nobs =    1 ... Value =
> -60.03
>
>  DIHEdral C_2  C_3  C_4  C_5     750.0 0   180.00 ! Nobs =    1 ... Value =
> -179.99
>
>  DIHEdral C_3  C_4  C_5  C_6     750.0 0   180.00 ! Nobs =    1 ... Value =
> -179.99
>
>
>
>  { Note: edit if necessary }
>
>  IMPRoper C_2  N_1  C_3  P_7     750.0 0  -35.000 ! Nobs =    1 ... Value =
> -37.817
>
>  IMPRoper P_7  C_2  O_8  O_9     750.0 0  -35.000 ! Nobs =    1 ... Value =
> -35.155
>
>
>
>  { Note: edit if necessary }
>
>  NONBonded N_1  0.2384  2.8509    0.2384  2.8509 ! assuming Nitrogen
>
>  NONBonded C_2  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
>  NONBonded C_3  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
>  NONBonded C_4  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
>  NONBonded C_5  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
>  NONBonded C_6  0.1200  3.7418    0.1000  3.3854 ! assuming Carbon
>
>  NONBonded P_7  0.5849  3.3854    0.5849  3.3854 ! assuming Phosphorous
>
>  NONBonded O_8  0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
>  NONBonded O_9  0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
>  NONBonded O_10 0.1591  2.8509    0.1591  2.8509 ! assuming Oxygen
>
>
>
>  set echo=true end
>
>
>
>
>
>
>
>
>
>


##############################################################################
Dr. Daan van Aalten                    Wellcome Trust Senior Fellow / Reader
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: see WWW page
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

Hi all,

I am trying to install cns on my new computer but there is an error
message:
sed: -e expression #1, char 11: Invalid range end
the architecture of the machine is unknown - CNS_ARCH=unknown-x86_64-Linux
aborting installation
make: *** [install] Error 1

If I leave out CNS_ARCH and specify it as linux then the following
error appears:
compiling: cc -O -ffast-math -DCNS_ARCH_TYPE_LINUX
C compiler passes test
compiling: fort77 -w -Nn2000 -O3  -funroll-loops -ffast-math
/bin/sh: fort77: command not found
linking: fort77
/bin/sh: fort77: command not found
/bin/sh: ./test_f: No such file or directory
***** ERROR: problem with Fortran compiler *****
make[3]: *** [fortran-test] Error 2
make[2]: *** [compiler-test] Error 2
make[1]: *** [compiler-test] Error 2
compiler problems - stopping installation
please check compilers before retrying installation
make: *** [install] Error 1

This seems to mean that I need to recompile my f2c library. But how do
I do that and what files do I need from NETLIB web site to do this.

Sorry for a basic question and looking forward to your help.
Thanks a lot,

Bojana Popovic

I do not think it is possible without writing some specia code
(perhaps someone can confirm this). However, I was wondering if you
would start a set of calculations on different CPU's with different
initial starting velocities (via the randoom number seed), then would
that act as a sort of "pseudo parallelisation" scheme?
Cheer
Mike

--- In cnsbb@yahoogroups.com, "chi_shy_guy" <chi_shy_guy@y...> wrote:
>
> Hi,
>
>   I currently trying to simulate some proteins, and I would like to
> parallize the CNS code (anneal.inp) to run on two or three processors.
> Has anyone done this? Any help is appreciated!
>
> Thanks,
> Steve
>

Hello,
I have a pdb structure generated from Dyana.
When I tried to convert it to CNS using generate_easy.inp, I noticed
that the generate_easy.inp has the following message:
  %READC-ERR: atom      1    GLY  HN   not found in molecular structure
  %READC-ERR: atom      1    GLY  1HA  not found in molecular structure
... ...

However, CNS compatible pdb and mtf file were generated. Should I be
worried about this warning message? If so, is there a program which
can convert pdb in Dyana format to CNS format? Or I should do the
modification manually?

Thanks in advance for any suggestions!

Daoning Zhang, Ph.D.
University of Maryland

Hi, all,

I got rotation angles in theta1, theta2 and theta3 from the
cross-rotation search. Now I would like to apply some of these angles to
my model. However, the realspace-transform.inp only takes real-space
rotation matrix. So my question is how to convert those angles to
matrix? seems that rotmat in CCP4 can do it, but I am a little confused
about the angle definition in it. Any other program can do it?

Thanks in advance.

Steve Xu
LBL

Hi,

the "special code" would mean insertion of OpenMP directives into the CNS source
code.
In trivial cases, this can be done automatically by a compiler, e.g. the ifort
compiler has a -parallel option which does exactly this.
However, to achieve a significant speedup of CNS, one needs to analyze and
understand the source code to find the top level where the OpenMP
parallelization could be established.
As a start, I would compile CNS with ifort's -qp option and find out which
routines consume most of the CPU time. Those are the ones that deserve
parallelization.
I do have OpenMP code for the structure-factor calculation stuff and it does
speed things up. However, this kind of source code modification cannot easily be
   distributed (if I understand correctly) due to the somewhat special licensing
situation of CNS. Someone please correct me if I'm wrong.

Kay


ozzy672003 wrote:
> I do not think it is possible without writing some specia code
> (perhaps someone can confirm this). However, I was wondering if you
> would start a set of calculations on different CPU's with different
> initial starting velocities (via the randoom number seed), then would
> that act as a sort of "pseudo parallelisation" scheme?
> Cheer
> Mike
>
> --- In cnsbb@yahoogroups.com, "chi_shy_guy" <chi_shy_guy@y...> wrote:
>
>>Hi,
>>
>>  I currently trying to simulate some proteins, and I would like to
>>parallize the CNS code (anneal.inp) to run on two or three processors.
>>Has anyone done this? Any help is appreciated!
>>
>>Thanks,
>>Steve
>>
>
>
>
>
>
>
>
>
>
> --------------------------------------------------------
> List information at http://groups.yahoo.com/group/cnsbb.
> Posting is only allowed for members of this list.
>
>
> Yahoo! Groups Links
>
>
>
>
>
>
>


--
Kay Diederichs   http://strucbio.biologie.uni-konstanz.de/~kay
email: Kay.Diederichs@...  Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

Check the .mtf file and .pdb file to make sure atoms
have the same name and numbering in these two files.

--- zdn3023 <zdn3023@...> wrote:

> Hello,
> I have a pdb structure generated from Dyana.
> When I tried to convert it to CNS using
> generate_easy.inp, I noticed
> that the generate_easy.inp has the following
> message:
>  %READC-ERR: atom      1    GLY  HN   not found in
> molecular structure
>  %READC-ERR: atom      1    GLY  1HA  not found in
> molecular structure
> ... ...
>
> However, CNS compatible pdb and mtf file were
> generated. Should I be
> worried about this warning message? If so, is there
> a program which
> can convert pdb in Dyana format to CNS format? Or I
> should do the
> modification manually?
>
> Thanks in advance for any suggestions!
>
> Daoning Zhang, Ph.D.
> University of Maryland
>
>
>
>




__________________________________
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Dear all,

I am installing cns on redhat enterprise V3. The "make g77install" ran
successfully. However, "source cns_solve_env" gave the following error message:

bash: setenv: command not found
bash: setenv: command not found
bash: setenv: command not found
bash: cns_solve_env: line 39: syntax error near unexpected token
` setenv'
bash: cns_solve_env: line 39: ` if ( ! $?CNS_ARCH ) setenv CNS_ARCH
` $CNS_SOLVE/bin/getarch`

Then I tried "csh" as suggested by previous messages, there seems to be no
response to "source cns_solve_env".

Then replacing

------------------
if ( -d $CNS_SOLVE ) then
if ( ! $?CNS_ARCH ) setenv CNS_ARCH `$CNS_SOLVE/bin/getarch`
else
setenv CNS_ARCH 'unknown'
endif
------------------

with
------------------
setenv CNS_ARCH 'intel-i686-linux'
------------------

did not solve the problem.

One more question is what is next if "source cns_solve_env" works.

Many thanks to your help.

Regards,

Longsheng lai