Hi

Just want to know is there any easy way to make
anomalous file for wavelength other than that of
Cu/Mo, which are included in CNS's library?  Thanks




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Hi folks,

I asked too soon. I needed to edit the protein.link file.

Cheers

J

Hello again,

I'm adding an unnatural amino acid in to my protein but unfortunately I
get this error below. I have added in the appropriate topology as a
normal aminoi acid (see below) but I cannot work out the problem. I
realise there is a problem with the recognition of the peptide linkage
but I just can't work out the fix.

Any help would be great

Joel

Program version= 1.1 File version= 1.1
SEED= 0.10557E+10
POWELL: number of degrees of freedom=  5136
NBONDS: generating intra-molecular exclusion list with mode= 5
MAKINB: mode   5 found   3632 exclusions and   2314 interactions(1-4)
%atoms "    -67  -ABA -C   " and "    -68  -GLY -N   " only  1.34 A apart
%atoms "    -95  -ABA -C   " and "    -96  -THR -N   " only  1.33 A apart
%atoms "    -167 -ABA -C   " and "    -168 -GLY -N   " only  1.33 A apart
%atoms "    -195 -ABA -C   " and "    -196 -THR -N   " only  1.33 A apart
NBONDS: found    43472 intra-atom interactions

Topology
RESIdue ABA

GROUp
ATOM N    TYPE NH1    CHARge=-0.35 END ! Nr of Hs =  1
ATOM H    TYPE=H      CHARge= 0.25   END
ATOM CA   TYPE CH1E   CHARge= 0.10 END ! Nr of Hs =  1
ATOM CB   TYPE CH2E   CHARge  0.0  END ! Nr of Hs =  2
ATOM CG   TYPE CH3E   CHARge  0.0  END ! Nr of Hs =  3
ATOM C    TYPE C      CHARge= 0.55 END ! Nr of Hs =  0
ATOM O    TYPE O      CHARge=-0.55 END ! Nr of Hs =  0

BOND  N    CA
BOND  CA   CB
BOND  CA   C
BOND  CB   CG
BOND  C    O
BOND  N    H


{ edit these DIHEdrals if necessary }
   DIHEdral  N    CA   CB   CG ! flexible dihedral ???    54.06

{ edit these IMPRopers if necessary }
IMPRoper  CA   N    C    CB  ! chirality or flatness improper    30.42

{ edit any DONOrs and ACCEptors if necessary }

END { RESIdue ABA }


--
Joel Tyndall, PhD

National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Ph +64 3 4797293
Fax +64 3 4797034

This is a lot more difficult than it seams.  It took me several months to
attach my PLP cofactor to a Lysine residue.  In fact it was such a pain that
I wrote down the whole procedure on my website so I would not forget:

http://www.personal.rdg.ac.uk/~sas01app/page32.html

I hope this is of some help.

Alan


>From: "bill1116.tw" <pong@...>
>To: cnsbb@yahoogroups.com
>Subject: [cnsbb] how to make covalent linkage
>Date: Wed, 19 May 2004 11:36:13 -0000
>
>Dear CNS users,
>I have a problem in connecting methyl group of small compound
>with the sulfide in Cys residue of my protein. How should I do making
>script in the generate.inp file to give any covalent linkage between
>methyl group and Cys
>

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Hi

my name is arangs.i am new to this group.recently joined.this group is
very nice.I have one doubt in NMR.I need to calculate the average pdb
file for protein nmr.how to do this.

I have choosen one pdb file .It has 60 strucures.I need one average
pdb file.how to get this.please give idea

arangs

CNS has a flag in its structure calculation protocols that asks you whether you
want an average structure after the calculation is done. Otherwise you can do it
on MOLMOL.

Munia

-----Original Message-----
From: arangsnmr [mailto:arangsnmr@...]
Sent: Sun 5/23/2004 11:12 PM
To: cnsbb@yahoogroups.com
Cc:
Subject: [cnsbb] nmr structure average

Hi

my name is arangs.i am new to this group.recently joined.this group is
very nice.I have one doubt in NMR.I need to calculate the average pdb
file for protein nmr.how to do this.

I have choosen one pdb file .It has 60 strucures.I need one average
pdb file.how to get this.please give idea

arangs



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Hello All,

I have been looking at numerous packages all day and I am trying to
figure out which one would be best for a very simple exercise. Namely,
I would like to mutate my protein and then calculate its energy after
some minimization. I noticed that CNS uses only "repulsive" terms. I
would like to use not only repulsive terms, but also electrostatic
terms, hbonding, etc. I looked for some  of these types of inclusive
parameter files and found nothing that worked. E.G. trying
"parallh22x.pro" from x-plor in CNS gave errors like this:

   %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%%
    bond energy constant missing.
    target bond length missing.
    ATOM1: SEGId="N   ",  RESId="678 ",  NAME="C   ",  CHEMical="C   "
    ATOM2: SEGId="N   ",  RESId="678 ",  NAME="OXT ",  CHEMical="OC  "
   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

I do not wish to puzzle over things like this indefinitely and reinvent
the wheel yet again.

I looked at namd and charmm, but had no idea where to start. I think
these packages in general expect a preexisting level of expertise with
said packages. So, before I waste a lot of time learning the vast
minutiae of these programs irrelevant to my goal, I thought I'd ask.
Any suggestions with references to simple tutorials would help. Again,
I don't want to model a mouse in silico or master the most
sophisticated molecular dynamics program ever conceived, I just want to
calculate a "state of the art" energy quickly and easily.

James

---------------------------------------------------------
James Stroud
Department of Chemistry
University of Colorado
Boulder, CO  80309-0215, USA

tel:  303-492-4503
www:  http://JamesStroud.com/
--------------------------------------------------------

Hi folks,

Err I have managed to fix my previous problem....I was miising a few
lines on the bottom of my inp file!

Sorry for clooging up the board

Joel

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Ph +64 3 4797293
Fax +64 3 4797034

Hi folks,

I thought I was doing so well but now I'm stumped. I am running
generate.inp to test patches I have set up for an unusual ligand. it all
goes well but just stops. (see error). Any suugestions would be much
appreciated.

  CNSsolve>     {- start parameter for the side chain building -}
  CNSsolve>     parameter
  CNSsolve>       nbonds
  CNSsolve>         rcon=20. nbxmod=-2 repel=0.9  wmin=0.1 tolerance=1.
  CNSsolve>         rexp=2 irexp=2 inhibit=0.25
  CNSsolve>       end
  CNSsolve>     end
  CNSsolve>
  CNSsolve>     {- Friction coefficient, in 1/ps. -}
  CNSsolve>     do (fbeta=100) (store1)
  CNSsolve>
  CNSsolve>     evaluate ($bath=300.0)
  CNSsolve>     evaluate ($nstep=500)
  CNSsolve>     evaluate ($timestep=0.0005)
  CNSsolve>
  CNSsolve>     do (refy=mass) (store1)
  CNSsolve>
  CNSsolve>     do (mass=20) (store1)
  CNSsolve>
  CNSsolve>     igroup interaction
  CNSsolve>       (store1) (store1 or known)
  CNSsolve>     end
  CNSsolve>
  CNSsolve>     {- turn on initial energy terms
  %NEXTF-ERR: EOF or ERROR encountered on input:

  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  PRIEND:    2 levels not terminated
              LEVEL=   1 KEY=CNSsolve>        ACTION=GO
              LEVEL=   2 KEY=IF               ACTION=SCAN
           ============================================================
            Maximum dynamic memory allocation:      221456 bytes
            Maximum dynamic memory overhead:            88 bytes


Cheers

Joel

--
Joel Tyndall, PhD

Lecturer
National School of Pharmacy
University of Otago
PO Box 913 Dunedin
New Zealand
Ph +64 3 4797293
Fax +64 3 4797034

Dear All,

I am trying to fit TFE, in my protein using CNS.
However ,  when I am minimizing I get the following
error:

   %XRASSOC-ERR: missing SCATter definition for ( F
ETF  1940 F1   ) chemical=F_4
  %XRASSOC-ERR: missing SCATter definition for ( F
ETF  1940 F2   ) chemical=F_5
  %XRASSOC-ERR: missing SCATter definition for ( F
ETF  1940 F3   ) chemical=F_6
  %XRASSOC error encountered: missing SCATter
definition for SELEcted atoms.
    (CNS is in mode: SET ABORT=NORMal END)

any suggestions please??

Tnank you,

Ashlesha.




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Dear all,
I have a dataset with selenium atoms to 2.6 A resolution (6 Se atoms detected by
mass spectrometry for 354 residues).

The data were treated with mosflm, and ccp4, and treated in p3121 and p3221.

When i do an anomalous difference patterson map, i obtain several peaks at 4
sigma. But the problem is that i can't find their corresponding peaks in the
patterson_map.list !!!!

Could someone help me?
thanks in advance


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Dear all,

I have been using CNS a lot in crystallography but not for MD.
I wonder if anyone could help me with this.

I have a structure and I would like to run a constant temperature
torsional MD.  What I am interested in is to obtain an average value of
the solvent accessibility of a particular residue, over the many
snapshot structures of the MD.  Is there an easy way of doing this?

Thank you very much.

Wai

--
Yu Wai Chen, PhD................................................
University of Cambridge                          +44-1223-766739
Department of Genetics, Downing Street, Cambridge  CB2 3EH, U.K.

Hello CNS/Xplor users,

I have been using CNS to calculate structures for several years now
and I am trying to switch platforms from windows (shudder) over to
linux. Xplor-NIH seems like it might be a relatively easy means to
acomplish this switch.

I understand that the *.psf files are analogous to the *.mtf files
used by CNS in that they contain topological info etc. As I recall,
CNS uses the generate_seq.inp input file to generate an mtf and pdb
file from a sequence text file such as ADE URI GUA CYT. Searching
through the Xplor-NIH tutorials, I have found numerous input files for
generating *.psf files from *.pdb input (generatedna.inp for example)
but none for generating the *.psf from text sequence info. Any help
pointing to the correct input file would be useful.

Alternatively, I could make my own script by modifying a length of
code for protein segment construction to be as follows:

segment
    name="RNA"
    chain
       LINK NUC  HEAD - *  TAIL + *  END
       FIRST  5PHO  TAIL + * END
       LAST 3TER  HEAD - * END
       sequence ADE URI GUA CYT end
    end
  end

My problem is that I can't figure out how to write this to output to a
*.psf file (having been somewhat spoiled by the conveniently
pre-generated "generate_seq.inp" file of CNS).

Any help that anyone can provide would be appreciated.

Tom Leeper

Hi, everyone!
Several weeks ago, I get a solve from a native x-ray data of a
protein using amore though the search model protein shows low
similarity (<20%identity) to my protein. But when being refined in
CNS, it always had high rfree (>50%). So I give up after a week hard
working.
Now, I solve the structure of my protein using MAD. And I using this
new structure as search model to get a solve from the original
native data. To my surprised, the struture can superpostition with
the old solve very well aside from some connecting loops.
Any idea of these?

Hallo,

thanks to all for the help with the psf file of sulfotyrosine.

Now I have a question not connected to cns.
Does anybody know the extinction coefficient for sulfotyrosine?

Thanks,

Sabine

--
********************************************
Sabine Ruth Quadt
Weizmann Institute of Science
Department of Structural Biology
76100 Rehovot
Israel

Tel: 00972-8-934-2152
Fax: 00972-8-934-4136
e-mail: sabine.quadt@...
********************************************

Hi Alex,
Sorry, I am not going to offer you a straightforward solution.
But I had exactly the same problem a few months ago.
Both f2mtz and sftools complained because of the scientific notation
used in the CV file which messes up the line format, spacing etc.
Finally, a friend helped me out by converting the CV file using a PYTHON
script
to a format that sftools and f2mtz are happy with.
Foll. this conversion, everything worked fine.
I can share the script with you, if you want.
Catch hold of a Python guru nearby if you are not one.
Raji
P.S.: I wish the program developers would fix this bug.


>===== Original Message From Xray Questions <xray_questions@...> =====
>***  For details on how to be removed from this list visit the  ***
>***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>Hi all:
>
>I am trying to change a cns.cv file to mtz.  I've done
>it multiple times with no problems but this time I
>have a data set in which a couple of reflections have
>too big an IOBS value.  These values make their lines
>FORMAT different from the rest and f2mtz reports an
>error reading these lines.  Is there a way to come
>around this problem???  Here is a piece of the data
>with the last line having the problem (notice how
>FORMAT for (0,0,13) is different b/c of .127506E+06):
>
> INDE     0    0  -11 IOBS= 42603.400 SIGI=  2159.500
>FOBS=   206.410
>                   SIGMA=     5.300 TEST=         0
> INDE     0    0  -12 IOBS=  1968.000 SIGI=   120.900
>FOBS=    44.360
>                   SIGMA=     1.380 TEST=         0
> INDE     0    0  -13 IOBS=     .127506E+06 SIGI=
>6423.000 FOBS=   357.080
>                   SIGMA=     9.110 TEST=         0
>
>
>Thanks in advance for any suggestions,
>
>Alex
>
>
>
>
>__________________________________
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Raji Edayathumangalam
Dept. of Biochemistry & Molecular Biology
Colorado State University
Fort Collins, CO 80523 USA
Tel:(970)491-4614
Fax:(970)491-0494

Hi all:

I am trying to change a cns.cv file to mtz.  I've done
it multiple times with no problems but this time I
have a data set in which a couple of reflections have
too big an IOBS value.  These values make their lines
FORMAT different from the rest and f2mtz reports an
error reading these lines.  Is there a way to come
around this problem???  Here is a piece of the data
with the last line having the problem (notice how
FORMAT for (0,0,13) is different b/c of .127506E+06):

  INDE     0    0  -11 IOBS= 42603.400 SIGI=  2159.500
FOBS=   206.410
                    SIGMA=     5.300 TEST=         0
  INDE     0    0  -12 IOBS=  1968.000 SIGI=   120.900
FOBS=    44.360
                    SIGMA=     1.380 TEST=         0
  INDE     0    0  -13 IOBS=     .127506E+06 SIGI=
6423.000 FOBS=   357.080
                    SIGMA=     9.110 TEST=         0


Thanks in advance for any suggestions,

Alex




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Hi,

I personally have a procedure that I always use for conversion to MTZ
files starting from CNS/XPLOR files:

first I remove all character streams (using vi, e.g. %s/INDE//g)
then I have a free format compatible ASCII file which is much much easier
to deal with! Use your favourite program to insert the data into an MTZ
file afterwards (free format reading is much easier to deal with than
formatted input).

Hope this helps.

Fred.

--

s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
         Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
         41 rue Jules Horowitz
         38027 Grenoble Cedex 01
         France
Tel:    (+33) (0) 438789605
Fax:    (+33) (0) 438785494
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   if I could, but I can't" (L.R., 1998)          (to live is to enjoy)
  =====================================================================
BEGIN_ELECTRONIC_SIGNATURE
M/R-:@ZF:!H)4!":,+WW$O;CZMD.9)UDE'9=GB8HB/]>X><9JL0+B,:..\_@J
MP/H/0?*ZM_GS&C'30I,>S1G3UI>T-H;`!!>N'*JT1?[?;#OW[]UR'@YY2X`Z
MN)5"J6`$X-<O3Q/),4@]C=2$")KC"37!"Z1L]XW(-8E&KIE9/0[=K]@C3[-#
?79H.\3W6F8,D<4WH4D.]E.>U+FCGZ3L6+P0_(.@T$```
END_ELECTRONIC_SIGNATURE

hi,

if you are happy just having h, k, l, Fobs, Sigma and Test, then dataman can
do this for you:

  DATAMAN > re m1 <infile> cns
  DATAMAN > wr m1 <outfile> hkl

you can then pass the ascii output file through f2mtz to get an mtz file

--dvd


> I am trying to change a cns.cv file to mtz.  I've done
> it multiple times with no problems but this time I
> have a data set in which a couple of reflections have
> too big an IOBS value.  These values make their lines
> FORMAT different from the rest and f2mtz reports an
> error reading these lines.  Is there a way to come
> around this problem???  Here is a piece of the data
> with the last line having the problem (notice how
> FORMAT for (0,0,13) is different b/c of .127506E+06):
>
>  INDE     0    0  -11 IOBS= 42603.400 SIGI=  2159.500
> FOBS=   206.410
>                    SIGMA=     5.300 TEST=         0
>  INDE     0    0  -12 IOBS=  1968.000 SIGI=   120.900
> FOBS=    44.360
>                    SIGMA=     1.380 TEST=         0
>  INDE     0    0  -13 IOBS=     .127506E+06 SIGI=
> 6423.000 FOBS=   357.080
>                    SIGMA=     9.110 TEST=         0

******************************************************************
                         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.
******************************************************************

Thanks to everybody for the suggestions on how to deal
with exponential terms
when converting file.hkl to file.mtz format.  Here is
a summary of responses and
what worked for me (look at the end).

----------------------------------------------------------------------
From Joshua Warren:

> perl script that takes an arbitrary cns .hkl
> file
> and converts it to a format easily readable by f2mtz
(namely
> 3F6.0,nF12.3
> where n is the number of database items other than
h, k, and l which
> are
> in the input file, e.g. IOBS, FOBS, etc.)
>
> #!/usr/bin/perl
> $/="INDEx=";
> $dummy = <>;
> while(<>){
>         s/\w+=//g;
>         s/\n//g;
>         ($h, $k, $l, @temp) = split;
>         printf "%6d%6d%6d", $h, $k, $l;
>                foreach (@temp){
>                         printf "%12.3f", $_;
>                 }
>         print "\n";
> }

I thought I could try this as a last resort.

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

William Scott:

> Suggestion 1:
>
>What happens if you change .127506E+06
>
>to 127506.0   by hand?
>
>If it works, just do that.
>
>Suggestion 2:  Use the F's and forget the I's.

Too many reflections with this problem so changing
them by hand not an option.
Even if trying to use only F's and I's the exponential
terms in the line shift
the other terms too, making FORMAT a problem.

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

Gerard DVD Kleywegt:

>if you are happy just having h, k, l, Fobs, Sigma and
Test, then dataman can
>do this for you:
>
>DATAMAN > re m1 <infile> cns
>DATAMAN > wr m1 <outfile> hkl
>
>you can then pass the ascii output file through f2mtz
to get an mtz file

Did not try this since I dont have DATAMAN, but could
be an option.

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

Other people suggested editing the file with
traditional commands (maybe use vi,
etc)

Im more of a user than a programmer.  Thanks ccp4i
;o)
-----------------------------------------------------------------------------

What worked for me:

Two people (raji & Tim Fenn) suggested using a python
script.  Tim Fenn supplied
me with a link to his script which worked for me like
a charm.  Its very
straightforward to use and I had no problem changing
the modified file to mtz
format.  Since the script page is already posted in
the bb, I will post it here
again.

Tim Fenn:

>I had this problem a while ago, I ended up writing a
python script to
>cirumvent it - its at:
>
>   http://www.stanford.edu/~fenn/scripts.html
>
>Its a bit of a hack job and I haven't used it in
awhile, but it should
>still do the trick.

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


Thanks again to everybody,

Alex





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Hi all
         I am trying to find the geometry weight from "optimize_wa.inp".
I do have a protein-ligand complex. After few cycles of refinement,
the program hangs by giving



Program version= 1.1 File version= 1.1
  Torsion Topology>
  Torsion Topology> fix group ( &atom_rigid )
  SELRPN:  0 atoms have been selected out of 7520
  Torsion Topology>
  Torsion Topology> end
  Torsion Dynamics> nstep=0
  Torsion Dynamics> cmremove=true
  Torsion Dynamics> end
  -------------------------- Torsion Topology
-----------------------------------
  Closed bonding networks have been detected. The bonds between the
following atoms will not be constrained:
     %atoms "  -411 -S43 -OR2 " and "  -411 -S43 -C12
     %atoms "  -411 -S43 -C52 " and "  -411 -S43 -OR2


      The residue 411 is a ligand. I tried to fix it by increasing the
parameters torsion_maxtree and torsion_maxbond but no improvement. Any
help is greatly appreciated.


R.Velavan

I noticed the same thing with closed rings that I had in a peptide
that I was generating an ensemble of NMR structures for. On my Mac this
did hang up the CNS job, but when I ran the same thing on LINUX the
message continues like this:

-------------------------- Torsion Topology
-----------------------------------
  Closed bonding networks have been detected. The bonds between the
following
    atoms will not be constrained:

     %atoms "    -17  -ALA -C   " and "    -17  -ALA -CA
     %atoms "    -23  -HIS -C   " and "    -23  -HIS -CA
     %atoms "    -28  -TRP -C   " and "    -28  -TRP -CA

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

  -------------------------- Torsion Topology
-----------------------------------
            - Regenerating molecular topology ignoring closed loops -


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


and the job runs to completion. Before I switched machines I tried Cartesion
dynamics instead (in anneal.inp)- no errors to do with closed loops, but
all kinds of my NOE constraints could not be satisfied. It was a good
thing to have this "open" bond, because otherwise, depending on what the
initial structure looked like, the closed loops could get stuck in the
wrong orientation. I never did figure out why the jobs crashed on my mac,
but I wonder if a different version/compilation of CNS would solve your
problem.

Tara

Tara Sprules
Post-Doctoral Fellow
Department of Chemistry
University of Alberta
Edmonton, AB
Canada


On Mon, 7 Jun 2004, Velavan R wrote:

>
>
> Hi all
>         I am trying to find the geometry weight from "optimize_wa.inp".
> I do have a protein-ligand complex. After few cycles of refinement,
> the program hangs by giving
>
>
>
> Program version= 1.1 File version= 1.1
> Torsion Topology>
> Torsion Topology> fix group ( &atom_rigid )
> SELRPN:  0 atoms have been selected out of 7520
> Torsion Topology>
> Torsion Topology> end
> Torsion Dynamics> nstep=0
> Torsion Dynamics> cmremove=true
> Torsion Dynamics> end
> -------------------------- Torsion Topology
> -----------------------------------
> Closed bonding networks have been detected. The bonds between the
> following atoms will not be constrained:
>     %atoms "  -411 -S43 -OR2 " and "  -411 -S43 -C12
>     %atoms "  -411 -S43 -C52 " and "  -411 -S43 -OR2
>
>
>      The residue 411 is a ligand. I tried to fix it by increasing the
> parameters torsion_maxtree and torsion_maxbond but no improvement. Any
> help is greatly appreciated.
>
>
> R.Velavan
>
>
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Hello Folks,
I've been working on the refinement of the protein that contains an
mu-diiron-oxo center.  The CNS-suite does not contain the SCATter
constant for the is ligand, does anyone know where it can be obtained?
  Another question..I collected data the data for this complex at a
wavelength far from it's absorption edge (12.8 kev), so I didn't think
that anomalous scattering from this group would not be a problem, but
after I run a "fp_fdp_group.inp" my R factors improve.  I've read many
papers on the structural biology of proteins that contain this group
and the use of this sort of refinement is not mentions.  This may be
because their feo/protein atom ratio is much smaller.  My protein
contains one FeOFe group for every one hundred residues.  Should I
have to perform this refinement?  Is there any difference between
using two Fe3+ groups and one O2- versus one FeOFe group?
Thanks in advance,
Herschel

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Greetings and Salutations,

I have a question on resource limits and CNS.

We are running CNS 1.1 on a linux system running RedHat 9.0.

The hardware platform is a dual processor system with 3.5 GB of memory and
plenty of disk space.

First let me give you the relevant information from log files and systems
routines.

************************************************************
=====> From CNS Log File -- Last Lines <======
************************************************************

XMAPAL: allocating space for real space object.
   ALLHP: request for    20530804 bytes
   ---------------------------------------------------------
   There is not enough memory available to the program.
   This may be because of too little physical memory (RAM)
   or too little swap space on the machine. It could also be
   the result of user or system limits. On most Unix systems
   the "limit" command can be used to check the current user
   limits. Please check that the datasize, memoryuse and
   vmemoryuse limits are set at a large enough value.
   ---------------------------------------------------------
   %ALLHP error encountered: not enough memory available
     (CNS is in mode: SET ABORT=NORMal END)
   *****************************************************
   ABORT mode will terminate program execution.
   *****************************************************
   Program will stop immediately.
            ============================================================
             Maximum dynamic memory allocation:  2128759704 bytes
             Maximum dynamic memory overhead:          1904 bytes
             Program started at: 09:22:46 on 16-Jun-2004
             Program stopped at: 09:40:40 on 16-Jun-2004
             CPU time used:    1041.9500 seconds
            ============================================================


************************************************************
=====>   Output From Limit Command    <======
************************************************************
cputime             unlimited
filesize              unlimited
datasize            unlimited
stacksize          8096 kbytes
coredumpsize    unlimited
memoryuse       unlimited
vmemoryuse      unlimited
descriptors        1024
memorylocked   unlimited
maxproc            7168


************************************************************
=====>        Output From swapon -s       <======
************************************************************
Filename                        Type            Size    Used    Priority
/dev/hda6                       partition       4145360 4       -1
/wrk/swapfile                     file            8191992 0       -2


It seems to me there exists sufficient system resources to run CNS yet CNS
reports that it is unable to acquire the necessary memory to run?  Has
anyone experienced this kind of problem and if so what did you do?

Best regards,

Aaron

Hi,
We had a similar problem and turns out that the torsion parameters were
not set right (too high) in the input file consuming way too much
memory.
Change the torsion parameters to see what resources the program needs
(multiply the maxlength*maxtree*maxchain, I think!, sorry do not have
the input file in front of me) and match to what you have in your
system.

Hope this helps.


Balaji



-----Original Message-----
From: Aaron J. Greenwood [mailto:agreenwo@...]
Sent: Wednesday, June 16, 2004 1:31 PM
To:
Subject: [cnsbb] System Resource Limit Question

Greetings and Salutations,

I have a question on resource limits and CNS.

We are running CNS 1.1 on a linux system running RedHat 9.0.

The hardware platform is a dual processor system with 3.5 GB of memory
and
plenty of disk space.

First let me give you the relevant information from log files and
systems
routines.

************************************************************
=====> From CNS Log File -- Last Lines <======
************************************************************

XMAPAL: allocating space for real space object.
   ALLHP: request for    20530804 bytes
   ---------------------------------------------------------
   There is not enough memory available to the program.
   This may be because of too little physical memory (RAM)
   or too little swap space on the machine. It could also be
   the result of user or system limits. On most Unix systems
   the "limit" command can be used to check the current user
   limits. Please check that the datasize, memoryuse and
   vmemoryuse limits are set at a large enough value.
   ---------------------------------------------------------
   %ALLHP error encountered: not enough memory available
     (CNS is in mode: SET ABORT=NORMal END)
   *****************************************************
   ABORT mode will terminate program execution.
   *****************************************************
   Program will stop immediately.
            ============================================================
             Maximum dynamic memory allocation:  2128759704 bytes
             Maximum dynamic memory overhead:          1904 bytes
             Program started at: 09:22:46 on 16-Jun-2004
             Program stopped at: 09:40:40 on 16-Jun-2004
             CPU time used:    1041.9500 seconds
            ============================================================


************************************************************
=====>   Output From Limit Command    <======
************************************************************
cputime             unlimited
filesize              unlimited
datasize            unlimited
stacksize          8096 kbytes
coredumpsize    unlimited
memoryuse       unlimited
vmemoryuse      unlimited
descriptors        1024
memorylocked   unlimited
maxproc            7168


************************************************************
=====>        Output From swapon -s       <======
************************************************************
Filename                        Type            Size    Used    Priority
/dev/hda6                       partition       4145360 4       -1
/wrk/swapfile                     file            8191992 0       -2


It seems to me there exists sufficient system resources to run CNS yet
CNS
reports that it is unable to acquire the necessary memory to run?  Has
anyone experienced this kind of problem and if so what did you do?

Best regards,

Aaron




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> the torsion parameters were not set right (too high)

in my experience, cns exit messages will report if you must increase a
particular torsion angle MD parameter.

but if that actually fixes it, the next problem that comes up is probably
an 'increase MAXJNT' error message.  in that case, edit dtorsion_top.f
sothat MAXJNT is higher than default (7) and recompile.  i have no idea
how to calculate what value will be proper - it worked for me once, but i
also still have the problem that this thread originated from, and it isn't
solving it.  i suspect the g77install and/or P4 at the moment... or the
new sed...

-bryan