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