From: Florian Mrugalla (florian.mrugalla_at_uni-dortmund.de)
Date: Tue Aug 23 2011 - 10:14:24 CDT

Thank You for your help.

I did what you suggested, but unfortunately it did not work.

I included the unique resids with the code:
$sel set resid [$sel get serial]

My psf looks now like this:
-----psf file start --------------------------
PSF

       1 !NTITLE
 REMARKS VMD generated structure x-plor psf file

   12000 !NATOM
       1 X 1 AR AR AR 0.000000 39.9480 0
       2 X 2 AR AR AR 0.000000 39.9480 0
       3 X 3 AR AR AR 0.000000 39.9480 0
       4 X 4 AR AR AR 0.000000 39.9480 0
       5 X 5 AR AR AR 0.000000 39.9480 0
       6 X 6 AR AR AR 0.000000 39.9480 0
       7 X 7 AR AR AR 0.000000 39.9480 0
       8 X 8 AR AR AR 0.000000 39.9480 0
       9 X 9 AR AR AR 0.000000 39.9480 0
      10 X 10 AR AR AR 0.000000 39.9480 0
      11 X 11 AR AR AR 0.000000 39.9480 0
...
-----psf file end --------------------------

If I open and rewrite the file, I get the same broken pdb file as before.

> On Tue, Aug 23, 2011 at 8:41 AM, Florian Mrugalla
> <florian.mrugalla_at_uni-dortmund.de> wrote:
>> Dear VMD users,
>> I am currently working on the creation of a system comprised of a protein
>> and several argon atoms. Yet, I have already separate pdb/psf files for
both (protein and argon atoms). Now I have some issues during the
combination and generation of a pdb/psf (with psfgen).
>> The core problem points at a destruction of my argon atom including
pdb.
>> It is destroyed even if I only open end rewrite it with VMD  (see far
below).
>> So far, I have my Argon atoms in a pdb.
>> My pdb looks like this:
>> --------pdb file start-----------------
>> ATOM      1  AR  AR  X   1       1.880   5.136   3.415  1.00  0.00      X
>>  AR
>> ATOM      2  AR  AR  X   1       3.760   8.393   3.415  1.00  0.00      X
>>  AR
>> ATOM      3  AR  AR  X   1       1.880   7.307   4.950  1.00  0.00      X
>>  AR
>> ATOM      4  AR  AR  X   1       3.760  10.563   4.950  1.00  0.00      X
>>  AR
>> ATOM      5  AR  AR  X   1       5.640   5.136   3.415  1.00  0.00      X
>>  AR
>> ATOM      6  AR  AR  X   1       7.520   8.393   3.415  1.00  0.00      X
>>  AR
>> ATOM      7  AR  AR  X   1       5.640   7.307   4.950  1.00  0.00      X
>>  AR
>> ATOM      8  AR  AR  X   1       7.520  10.563   4.950  1.00  0.00      X
>>  AR
>> ...
>> --------pdb file end-----------------
>> to get the corresponding psf file I used the following TCL commands which
>> I found on the vmd mailing list.
>> -----start of commands--------------------------
>> set sel [atomselect top all]
>> $sel set segname X
>> $sel set type AR
>> $sel set resname AR
>> $sel set chain X
> please try adding a loop here that
> gives each argon atom a unique
> residue id and all the number 1.
> otherwise psfgen might think that
> all argon atoms belong to the same
> residue, yet it only knows one atom
> in that residue.
> cheers,
> axel.
>> animate write psf argon.psf waitfor all
>> ----end of commands-----------------------------
>> Now I have a psf file which looks like this:
>> -----psf file start --------------------------
>> PSF
>>       1 !NTITLE
>>  REMARKS VMD generated structure x-plor psf file
>>   12000 !NATOM
>>       1 X    1    AR   AR   AR     0.000000       39.9480           0  
    2 X    1    AR   AR   AR     0.000000       39.9480           0    
  3 X    1    AR   AR   AR     0.000000       39.9480           0      
4 X    1    AR   AR   AR     0.000000       39.9480           0       5
X    1    AR   AR   AR     0.000000       39.9480           0       6 X
   1    AR   AR   AR     0.000000       39.9480           0       7 X  
 1    AR   AR   AR     0.000000       39.9480           0 ...
>>       0 !NBOND: bonds
>>       0 !NTHETA: angles
>>       0 !NPHI: dihedrals
>>       0 !NIMPHI: impropers
>>       0 !NDON: donors
>>       0 !NACC: acceptors
>>       0 !NNB
>>       0       0       0       0       0       0       0       0       0
      0       0       0       0       0       0       0       0       0
      0       0       0       0       0       0       0       0       0
      0       0       0       0       0 ...
>>       1       0 !NGRP
>>       0       0       0
>> ----psf file end-----------------------------
>> When I use the following commands in the TCL console or in a TCL
script,
>> I get the results shown below.
>> -----start of commands--------------------------
>> package require psfgen
>> topology charmm.rtf
>> #load Ar
>> readpsf $ar_in_psf
>> coordpdb $ar_in_pdb
>> #write out the same files without doing anything
>> writepsf $out_temp_psf
>> writepdb $out_temp_pdb
>> -----end of commands--------------------------
>> My pdb looks like this:
>> --------pdb file start-----------------
>> ATOM      1  AR  AR  X   1     112.800  69.176  32.580  1.00  0.00    
 X AR
>> ATOM      2  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> ATOM      3  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> ATOM      4  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> ATOM      5  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> ATOM      6  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> ATOM      7  AR  AR  X   1       0.000   0.000   0.000 -1.00  0.00      X
>> --------pdb file end-----------------
>> I would be grateful if you could help me out with this issue.
>> Yours sincerely,
>> Florian
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.