Hi folks,

Trying to install cns on RHE3 (amd64) machine. I know it can be done I'm
just not smart enough to nut it out. I have sorted the architecture
error and my problem arises when I try to run Make install. I understand
that there is issues with the compilers and one is supposed to use g77
compilers with g77install. So I tried that and now I'm stuck.

Any help (as basic as possible) would be very much appreciated

Cheers

Joel

The error following % make install

sed: -e expression #1, char 11: Invalid range end
copying files in instlib directory g77-unix to amd-x86_64-linux_g77
arch_env
machine_c.c
machine_f.f
Makefile.header
>>>> WARNING: this is an unsupported machine type
making source directory in amd-x86_64-linux_g77
making bin directory in amd-x86_64-linux_g77
making utils directory in amd-x86_64-linux_g77
making test directory in amd-x86_64-linux_g77
linking source files to amd-x86_64-linux_g77/source
linking machine_f.f to source directory
linking machine_c.c to source directory
linking generic fft file to source directory
making Makefile in source directory
making compiler-test directory in amd-x86_64-linux_g77
testing Fortran and C compilers
compiling: gcc -O -ffast-math -DCNS_ARCH_TYPE_G77_UNIX
/usr/bin/ld: skipping incompatible
/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libc.so when
searching for -lc
/usr/bin/ld: skipping incompatible
/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libc.a when
searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc
/usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc
/usr/bin/ld: cannot find -lc
collect2: ld returned 1 exit status
/bin/sh: line 1: ./test_c: No such file or directory
***** ERROR: problem with C compiler *****
make[3]: *** [c-test] Error 3
compiling: g77 -fno-globals -Wno-globals -O3  -funroll-loops -ffast-math
linking: g77 -w
/usr/bin/ld: skipping incompatible
/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libm.so when
searching for -lm
/usr/bin/ld: skipping incompatible
/usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libm.a when
searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm
/usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm
/usr/bin/ld: cannot find -lm
collect2: ld returned 1 exit status
/bin/sh: line 1: ./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: *** [g77install] Error 1

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

sir, Trying run aria to caculate protein structure, following message
were displayed. I need help,thanks a lot!



Traceback (innermost last):
   File "/prog/aria/aria1.2/Aria/RunAria.py", line 574, in ?
     new['WHICH_PEAKS_1'], new['VOL_OR_INT_1'])
   File "/prog/aria/aria1.2/Aria/DataIO/ConvertData.py", line 100, in
Sparky2Aria
     PPM.WriteChem(chemFile)
   File "/prog/aria/aria1.2/Aria/DataIO/PpmList.py", line 1129, in
WriteChem
     midshift = string.atof(EACH.shift)
ValueError: invalid literal for atof(): 13C

Dear all:

We developed a novel loop prediction method and
validated on a number of crystal structure
successfully. However, when working on an
intracellular loop (11 a.a.) of a membrane protein, we
found a structure which is 40 kcal lower than the
crystal structure after energy minimization (rmsd=4.6
angstrom). And the unit cell calculations showed that
there is no crystal packing effect in this case. Could
anyone enlighten me what’s the possible reason for
these?

Thanks,
Simon




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Some thoughts:

1)  Being a membrane protein, the crystallization conditions are
probably odd.  When you minimized, did you use a dielectric constant
approriate to the 1% beta-octylglucoside or whatever other nonsense
they needed to obtain a crystal?

2) Or are there discrete detergent or solvent molecules bound to the
loop?  Sometimes these molecules need to be considered to be part of
the structure.  Minimization sometimes gives a different answer if the
solvent molecules are left out.  Although there are better examples, a
story I was involved in is a simple example I know offhand.  See:

Puius et al. Biochemistry. 1998 Jun 30;37(26):9258-65.
http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi9727287

Kim, HW at al. Bull. Korean Chem. Soc. 2001, Vol. 22, No. 3
http://newjournal.kcsnet.or.kr/main/ j_search/j_download.htm?code=B010302

3) Was it an older, lower-resolution structure, or did the loop have
very high B-factors?  The formal possibility exists is that the loop
is mistraced, or an error was made in connectivity.

4) If the structure factors are deposited for this structure, you can
calculate the electron density and inspect the maps!

Good luck,
Y

--
Yoram A. Puius, M.D., Ph.D.
y.puius@...
Fellow, Division of Infectious Diseases
Columbia Presbyterian Medical Center


On 6/10/05, Xiang(Simon) Wang <sim_wang@...> wrote:
> Dear all:
>
> We developed a novel loop prediction method and
> validated on a number of crystal structure
> successfully. However, when working on an
> intracellular loop (11 a.a.) of a membrane protein, we
> found a structure which is 40 kcal lower than the
> crystal structure after energy minimization (rmsd=4.6
> angstrom). And the unit cell calculations showed that
> there is no crystal packing effect in this case. Could
> anyone enlighten me what's the possible reason for
> these?
>
> Thanks,
> Simon
>

> 3) Was it an older, lower-resolution structure, or did the loop have
> very high B-factors?  The formal possibility exists is that the loop
> is mistraced, or an error was made in connectivity.
>
> 4) If the structure factors are deposited for this structure, you can
> calculate the electron density and inspect the maps!

yoram is absolutely right, of course. i just wanted to add that if the
structure factors were deposited, there's a good chance that the electron
density maps (as well as per-residue and overall statistics about the
temperature factors and the fit of the model to the density) are available
from the uppsala electron-density server, EDS (http://eds.bmc.uu.se/). for
instance, the entry for pdb entry 1CBS can be found at:
http://eds.bmc.uu.se/cgi-bin/eds/uusfs?pdbCode=1cbs

if structure factors were not deposited, you can get possibly useful
information about the quality of the model (or the regions of interest) from
the PDBREPORT database. for instance, the entry for 1CBS lives at:
http://www.cmbi.kun.nl/cgi-bin/nonotes?1cbs

--gerard

******************************************************************
                          Gerard J.  Kleywegt
      [Research Fellow of the Royal  Swedish Academy of Sciences]
Dept. of Cell & Molecular Biology  University of Uppsala
                  Biomedical Centre  Box 596
                  SE-751 24 Uppsala  SWEDEN

      http://xray.bmc.uu.se/gerard/  mailto:gerard@...
******************************************************************
     The opinions in this message are fictional.  Any similarity
     to actual opinions, living or dead, is purely coincidental.
******************************************************************

I am running CNS on a Mac OSX 10.3.9.  My dihedral energies are too high when I
check
the output files for all of my dihedral restraints, I get

========================================
  B    330  ILE  C
  B    331  ASN  N
  B    331  ASN  CA
  B    331  ASN  C
  Dihedral=    0.000  Energy=   -1.994 C=    1.000 Equil=  -67.000 Delta=
-687.549
  Range=  18.000 Exponent=  2
  ========================================
  B    338  TRP  C
  B    339  LYS  N
  B    339  LYS  CA
  B    339  LYS  C
  Dihedral=    0.000  Energy=   -1.994 C=    1.000 Equil= -142.000
Delta=-1031.323
  Range=  44.000 Exponent=  2
  ========================================
  B    339  LYS  C
  B    340  VAL  N
  B    340  VAL  CA
  B    340  VAL  C
  Dihedral=    0.000  Energy=   -1.994 C=    1.000 Equil= -121.000
Delta=-2521.014
  Range=  30.000 Exponent=  2
  ========================================

The dihedral value is given as zero and the delta value is too high the  input
files have the
format


assign ( resid 330 and name c and segid  b  ) ( resid 331 and name n and segid 
b   )
        ( resid 331 and name ca and segid  b  ) ( resid 331 and name c and segid 
b   ) 1.0
-67.00  18.00 2
assign ( resid 338 and name c and segid  b  ) ( resid 339 and name n and segid 
b   )
        ( resid 339 and name ca and segid  b  ) ( resid 339 and name c and segid 
b   ) 1.0
-142.00  44.00 2
assign ( resid 339 and name c and segid  b  ) ( resid 340 and name n and segid 
b   )


Has anyone seen this?

Hi folks,

Having managed to refine my structure I have hit a wall when trying to
run xtal_pdbsubmission.inp.

My problem is I don't know the syntax to input the chain ids under atom
selection. There are multiple chains, with ligands, waters and ions, all
with a separate chain id. An example file would be invaluable or any
other help appreciated.

Regards

Joel

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

Dear folks,

I tried to install CNS 1.1 to my Redhat 9 Linux
system. I got the following error message. I am new to
CNS and Linux. I will highly appreciate if any of you
could help me out.

Error message I got:
______________________________________________________
[root@localhost cns_solve_1.1]# make install
copying files in instlib directory linux to
intel-i686-linux
arch_env
machine_c.c
machine_f.f
Makefile.header
Makefile.header.pgf77
making source directory in intel-i686-linux
making bin directory in intel-i686-linux
making utils directory in intel-i686-linux
making test directory in intel-i686-linux
linking source files to intel-i686-linux/source
linking machine_f.f to source directory
linking machine_c.c to source directory
linking generic fft file to source directory
making Makefile in source directory
making compiler-test directory in intel-i686-linux
testing Fortran and C compilers
compiling: cc -O -ffast-math -DCNS_ARCH_TYPE_LINUX
/bin/sh: line 1: cc: command not found
/bin/sh: line 1: ./test_c: No such file or directory
***** ERROR: problem with C compiler *****
make[3]: *** [c-test] Error 3
compiling: fort77 -w -Nn2000 -O3 -malign-double
-funroll-loops -ffast-math
/bin/sh: line 1: fort77: command not found
linking: fort77
/bin/sh: line 1: fort77: command not found
/bin/sh: line 1: ./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
[root@localhost cns_solve_1.1]#
______________________________________________________




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Dear CNS users:

I have alternate conformations in my pdb. I searched through the archives to
see how I can refine alternate conformations using CNS but the procedure
wasn't clear to me.

Can somebody send me a sample pdb input for CNS and outline the procedure for
refining alternate conformations in CNS.

Thanks in advance,

Akanksha
--
Ph.D. Candidate,
School of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta, GA 30332

Call For Speakers

Gordon Research Conference on Diffraction Methods in Structural Biology
           July 16-21, 2006 Bates College, Lewiston, Maine, USA

                 Co-Chairs:  Paul Adams & Elspeth Garman


The 2006 Gordon Research Conference on Diffraction Methods in Structural
Biology will encompass advances in the methodology for macromolecular
X-ray crystallography, and other diffraction/scattering applications.
Particularly significant structural results will be highlighted during
the meeting.  All participants will be expected to contribute
extensively to discussion, to present either a talk or a poster, and to
attend the entire conference.

Suggestions for topics, specific speakers, and any other aspect of the
meeting are kindly requested from you.  Please feel free to email either
Paul Adams (pdadams@...) or Elspeth Garman (elspeth@...)
with your ideas.  A sentence or two about the speaker or idea would be
most helpful.  You are encouraged to suggest yourself as a speaker or
anyone else.

--
==========================================================
| Paul Adams                                             |
| Staff Scientist, Physical Biosciences Division         |
| Head, Berkeley Center for Structural Biology           |
| Deputy PI, Berkeley Structural Genomics Center         |
|--------------------------------------------------------|
| Building 64, Room 248  | Lawrence Berkeley Laboratory, |
| Tel: 510-486-4225      | 1 Cyclotron Road,             |
| FAX: 510-486-5909      | BLDG 64R0121,                 |
| mailto:PDAdams@... | Berkeley, CA 94720, USA.      |
==========================================================

hi all,
I am trying to introduce a new residue into CNS (a carcinogen
covalently bound to dG). Can any one suggest me how do I go about doing
this.
Thanks in advance

Raviprasad Aduri

Hi Raviprasad,

The easiest might be to add stereochemical definitions for your residue to,
say, the DNA 'topology' and
'parameter' files in CNS. One can make them either manually (not recommended)
in CNS format or use
the HIC-Up server or the PRODRG server, which can give you starting
definitions files that can be easily
appended to existing CNS files. Beware though that some of these restraints
spit out by programs are
sometimes incorrect. The user needs to optimize the values as he/she proceeds
through refinement.

To make a covalent link of the residue to the dG, one can use the 'patch'
statement in the CNS files.

See the CNS website for the above - however cryptic some of it may sound, a
lot of this stuff is
discussed there.

Good luck.
Raji



>===== Original Message From cnsbb@yahoogroups.com =====
>There is 1 message in this issue.
>
>Topics in this digest:
>
>      1. non standard residues
>           From: "rpaduri" <rpaduri@...>
>
>
>________________________________________________________________________
>________________________________________________________________________
>
>Message: 1
>   Date: Thu, 14 Jul 2005 23:08:46 -0000
>   From: "rpaduri" <rpaduri@...>
>Subject: non standard residues
>
>hi all,
>I am trying to introduce a new residue into CNS (a carcinogen
>covalently bound to dG). Can any one suggest me how do I go about doing
>this.
>Thanks in advance
>
>Raviprasad Aduri

Raji Edayathumangalam
Postdoctoral Associate
The Rockefeller University
New York, NY 10021

Dear Sarah,

The error was from the script getarch in the $CNS_SOLVE/bin directory.
I just replace the following lines (line 38-42) from cns_solve_env:
------------------
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'
------------------

Kambo Wong
Department of Biochemistry
The Chinese University of Hong Kong


--- In cnsbb@yahoogroups.com, "Sarah Diane" <sdcady@i...> wrote:
> Hello
>
> Hopefully someone can help me out here.  We are trying to install CNS
> on linux Fedora Core 2.  We compiled using the g77 compiler because of
> the error in the other compiler for red hat systems.  However, when I
> try to do the "source cns_solve_env" command before running the
> software to set the environmental variables, it gives me the following
> error:
>
> sed: -e expression #1, char 11: Invalid range end
>
> Not sure if this is related to CNS needing to access the g77 version
> installed on the computer and not the native version.
>
> Many thanks, hopefully I can figure it out!
>
> Regards,
> Sarah Cady

Dear Joel,

I have recently install CNS1.1 on athlon64 in a FC3 box using intel
compilers. Basically, I followed the instruction from Joe Krahn
(http://home.nc.rr.com/krahnfamily/source/CNS_with_IFC.html Thanks
Joe!) and it worked without much problem.

Kambo Wong

--- In cnsbb@yahoogroups.com, Joel Tyndall <joel.tyndall@o...> wrote:
> Hi folks,
>
> Trying to install cns on RHE3 (amd64) machine. I know it can be done I'm
> just not smart enough to nut it out. I have sorted the architecture
> error and my problem arises when I try to run Make install. I understand
> that there is issues with the compilers and one is supposed to use g77
> compilers with g77install. So I tried that and now I'm stuck.
>
> Any help (as basic as possible) would be very much appreciated
>
> Cheers
>
> Joel
>
> The error following % make install
>
> sed: -e expression #1, char 11: Invalid range end
> copying files in instlib directory g77-unix to amd-x86_64-linux_g77
> arch_env
> machine_c.c
> machine_f.f
> Makefile.header
> >>>> WARNING: this is an unsupported machine type
> making source directory in amd-x86_64-linux_g77
> making bin directory in amd-x86_64-linux_g77
> making utils directory in amd-x86_64-linux_g77
> making test directory in amd-x86_64-linux_g77
> linking source files to amd-x86_64-linux_g77/source
> linking machine_f.f to source directory
> linking machine_c.c to source directory
> linking generic fft file to source directory
> making Makefile in source directory
> making compiler-test directory in amd-x86_64-linux_g77
> testing Fortran and C compilers
> compiling: gcc -O -ffast-math -DCNS_ARCH_TYPE_G77_UNIX
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libc.so when
> searching for -lc
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libc.a when
> searching for -lc
> /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching
for -lc
> /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching
for -lc
> /usr/bin/ld: cannot find -lc
> collect2: ld returned 1 exit status
> /bin/sh: line 1: ./test_c: No such file or directory
> ***** ERROR: problem with C compiler *****
> make[3]: *** [c-test] Error 3
> compiling: g77 -fno-globals -Wno-globals -O3  -funroll-loops -ffast-math
> linking: g77 -w
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libm.so when
> searching for -lm
> /usr/bin/ld: skipping incompatible
> /usr/lib/gcc-lib/x86_64-redhat-linux/3.2.3/../../../libm.a when
> searching for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching
for -lm
> /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching
for -lm
> /usr/bin/ld: cannot find -lm
> collect2: ld returned 1 exit status
> /bin/sh: line 1: ./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: *** [g77install] Error 1
>
> --
> Joel Tyndall, PhD
>
> Lecturer
> National School of Pharmacy
> University of Otago
> PO Box 913 Dunedin
> New Zealand
>
> Pukenga
> Te Kura Taiwhanga Putaiao
> Te Whare Wananga o Otago
> Pouaka Poutapeta 913 Otepoti
> Aotearoa
>
> Ph / Waea               +64 3 4797293
> Fax / Waeawhakaahua     +64 3 4797034

You need to get some new paramer and topology files (I suggest prodrg
from dundee) you will also need to set up a patch to link the new ligand
to dg. Or simply make new par and top files for a midified dg

Hope this helps

J

rpaduri wrote:

>hi all,
>I am trying to introduce a new residue into CNS (a carcinogen
>covalently bound to dG). Can any one suggest me how do I go about doing
>this.
>Thanks in advance
>
>Raviprasad Aduri
>
>
>
>
>
>--------------------------------------------------------
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>Posting is only allowed for members of this list.
>
>
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>
>
>
>
>
>
>
>
>

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand

Pukenga
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 913 Otepoti
Aotearoa

Ph / Waea               +64 3 4797293
Fax / Waeawhakaahua     +64 3 4797034

Dear board,

I have the same
sed: -e expression #1, char 11: Invalid range end
error on my Ubuntu installation that others have
recently seen on Fedora. I get the error sourcing
cns_solve_env in tcsh, but not in csh or zsh. All my
cns scripts run fine except for water_pick.inp, which
crashes every time with an error like, "zero atoms
selected." Are these two problems related?

Thanks,

Nate Nicely
Ph.D. candidate
NCSU Molecular & Structural Biochemistry




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Dear board,
I have the same
sed: -e expression #1, char 11: Invalid range end
error on my Ubuntu installation that others have
recently seen on Fedora. I get the error sourcing
cns_solve_env in tcsh, but not in csh or zsh. All my
cns scripts run fine except for water_pick.inp, which
crashes every time with an error like, "zero atoms
selected." Are these two problems related?
Thanks,
Nate Nicely
Ph.D. candidate
NCSU Molecular & Structural Biochemistry
	
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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
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Hi all,
Does anyone know how the dna-rna_restraints.def input file works,
because i keep on getting the following error when i read it into
anneal.inp under the {*DNA-RNA base planarity restraints file*} when i
set   {===>} nmr.plan.file="dna-rna_restraints_fred.def";
STDIH: allocating space for    1600 assignments.
  MESSage=OFF
  ECHO=FALSe {OFF}
  Program version= 1.1 File version= 1.1
  %PLANe-ERR: unrecognized command:
   for
   ^^^
  %PLANe-ERR: unrecognized command:
   for id
       ^^
  %PLANe-ERR: unrecognized command:
   for id in
          ^^
  %WDSUB-ERR: symbol not found:
   for id in $id
             ^^^
  %PLANe-ERR: unrecognized command:
   for id in $id
             ^^^
  %PLANe-ERR: unrecognized command:
   for id in $id (
                 ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( (
                   ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid
                     ^^^^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1
                           ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 :
                             ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14
                               ^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or
                                  ^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid
                                     ^^^^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2
                                           ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2 :
                                             ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2 : 13
                                               ^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2 : 13 )
                                                  ^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2 : 13 ) and
                                                    ^^^
  %PLANe-ERR: unrecognized command:
   for id in $id ( ( resid 1 : 14 or resid 2 : 13 ) and tag

...and so on.

FREDRICK
                                                        ^^^

Hi,

   I'm trying to simulate an ammonium transport protein(1U7G.pdb) and
it has a MSE residue which is not part of the "usual" protein-allhdg
topology and parameter files. I have found these files and inserted
the MSE .top and .param files into the protein-allhdg files but I
receive this error

  %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
   bond energy constant missing.
   target bond length missing.
   ATOM1: SEGId="    ",  RESId="12  ",  NAME="C   ",  CHEMical="C   "
   ATOM2: SEGId="    ",  RESId="13  ",  NAME="N   ",  CHEMical="N_1 "
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
   bond energy constant missing.
   target bond length missing.
   ATOM1: SEGId="    ",  RESId="13  ",  NAME="C   ",  CHEMical="C_3 "
   ATOM2: SEGId="    ",  RESId="14  ",  NAME="N   ",  CHEMical="N_1 "
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
..........................................

Can anyone help me with this problem???????

Thanks,
Steve

Trying to install cns1,1 on RHE3 (sgi altix 350, ) machine. Got the
error below.

Any help (as basic as possible) would be very much appreciated

# make install
sed: -e expression #1, char 11: Invalid range end
the architecture of the machine is unknown - CNS_ARCH=unknown-ia64-Linux
aborting installation
make: *** [install] Error 1

> # make install
> sed: -e expression #1, char 11: Invalid range end

This is a problem with the sed line in the script "getarch" in the
$CNS_SOLVE/bin directory:
MAJOR=`echo $RELEASE | sed -e 's/^V//' | sed -e 's/[A-z]\.//' | awk
'BEGIN{FS="."}{print $1*1}'`

Change it to:
MAJOR=`echo $RELEASE | sed -e 's/^V//' | sed -e 's/[A-Za-z]\.//' | awk
'BEGIN{FS="."}{print $1*1}'`

and sed will be much happier.

I'm not sure if you have additional issues with the install, since I don't use
IA64 machines.

Phil Jeffrey
Dept. Molecular Biology
Princeton University

Dear Users,

I want to do a energy minimization  for  trypsin-BPTI complex. I need
to add 15 Cl- ions in positions of largest electrostatic
potential and fix these counterions during all
simulations. Is it possible ?


Thanks,
Lakshmi

I have a question about the distance bounds produced by the mmdisg module in
CNS.

Starting with the trx_ example that is distributed with CNS, I stopped the
dg_sa.inp protocol by replacing the 'storebounds' with
'writebounds="trx.bounds"'.

When I look at the lower bounds produced this way, most of them are zero.  This
seems odd, since I would have thought that the van der Waals radii would lead
to
nonzero lower bounds.

Stranger yet, if I change the statement
   {===>} md.dg.type="sub";
in dg_sa.inp to
   {===>} md.dg.type="complete";
then I obtain lower bounds that are much larger than the upper bounds.

Any help would be greatly appreciated!

Michael Lewis


--

-----------------------------------------------------------------
Robert Michael Lewis  buckaroo@...
Department of Mathematics http://www.math.wm.edu/~buckaroo
College of William & Mary
P. O. Box 8795 		 (757) 221-2032
Williamsburg, Virginia 23187-8795 FAX: (757) 221-7400
-----------------------------------------------------------------

Second Call For Speakers

Gordon Research Conference on Diffraction Methods in Structural Biology
           July 16-21, 2006 Bates College, Lewiston, Maine, USA

                 Co-Chairs:  Paul Adams & Elspeth Garman

The 2006 Gordon Research Conference on Diffraction Methods in Structural
Biology will encompass advances in the methodology for macromolecular
X-ray crystallography, and other diffraction/scattering applications.
Particularly significant structural results will also be highlighted
during the meeting. All participants will be expected to contribute
extensively to discussion, to present either a talk or a poster, and to
attend the entire conference.

We have identified the following topic areas for the meeting.
Suggestions for specific speakers, and any other aspect of the meeting
are kindly requested from you. Please feel free to email either Paul
Adams (pdadams@...) or Elspeth Garman (elspeth@...) with
your ideas. A sentence or two about the speaker or idea would be most
helpful. You are encouraged to suggest yourself as a speaker or anyone
else.

- Membrane proteins and complexes
- X-ray data collection and data processing
- Other biophysical methods
- High throughput structure solution
- Phasing
- Electron microscopy, electron diffraction and neutron diffraction
- Difficult structures and challenging problems
- Advances in structure refinement
- Computational tools for structure completion

--
==========================================================
| Paul Adams,                                            |
| Staff Scientist, Physical Biosciences Division         |
| Head, Berkeley Center for Structural Biology           |
| Deputy PI, Berkeley Structural Genomics Center         |
|--------------------------------------------------------|
| Building 64, Room 248  | Lawrence Berkeley Laboratory, |
| Tel: 510-486-4225      | 1 Cyclotron Road,             |
| FAX: 510-486-5909      | BLDG 64R0121,                 |
| mailto:PDAdams@... | Berkeley, CA 94720, USA.      |
==========================================================

Try to install cns to sgi altix(itanium 2, rhe3). I make the change
with the getarch script (add the intel-ia64-linux id). first try the
command "make install", didn't work. Then try "make g77install" .
Although there is a warning " the computer system not supported",
the compilation is done. After  I test the cns, the message:

==================
%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: 10:52:34 on 09-Aug-2005
            CPU time used:       0.0039 seconds


I think the installation is not wrong. Would sombody help me.

Thanks

is there a way to get a list of noe violations for a set of
structures, showing which noes are consistantly violated etc.?

I know there is a list of violations for each structure in anneal.out,
but there is a torrent of info in there which makes it hard to do the
comparison over all structures..

thanks,

simon

There is a CNS script called noe_viol.inp which would calculate the violations
for each structure. But it works on one structure at a time. If you use ARIA
instead of CNS it automatically generates a list of noe violations for all
stuctures after the structure calculations are completed.

Good luck!

Munia

-----Original Message-----
From: cnsbb@yahoogroups.com on behalf of simoneinhorn
Sent: Wed 8/10/2005 10:33 AM
To: cnsbb@yahoogroups.com
Cc:
Subject: [cnsbb] noe violations
is there a way to get a list of noe violations for a set of
structures, showing which noes are consistantly violated etc.?

I know there is a list of violations for each structure in anneal.out,
but there is a torrent of info in there which makes it hard to do the
comparison over all structures..

thanks,

simon




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Hi,

I am using ARIA 2.0 to compute a structure and am running into some
problems.  If I use the CNS libraries that came with CNS1.1,
everything works fine except for the floating chirality assignments
that ARIA implements.  When I compile using ARIA 2.0 everyhting seems
to work, except the strcutures generated are not nearly as good and
the output for the floating assignm,ents seems ot merely list chiral
protons, rather than assign them.

I believe the problem maybe that I'm using the g77 compiler, so I'm
trying to get the fort77 compiler to work.  I seem to have run into
the error report on the cns main webpage, but I cannot seem to get the
fix to work.  The link they provide states
"To compile ccp4 on Linux, simply add

-fno-automatic

to the XFFLAGS in all the makefiles."

however I have no idea what this means.  I've been digging through all
the amkes files and cannnot find anything that seems to resemble "XFFLAGS"

Can anyone give me some advice here?

Steve