VMD-L Mailing List

From: Florian Mrugalla (florian.mrugalla_at_uni-dortmund.de)
Date: Tue Aug 23 2011 - 07:41:02 CDT

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

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