VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 23 2011 - 09:33:39 CDT

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.