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From: Florian Mrugalla (florian.mrugalla_at_uni-dortmund.de)
Date: Tue Aug 23 2011 - 07:41:02 CDT
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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
- Next message: John Stone: "Re: making movie"
- Previous message: Moeed: "Re: visualizing unrealistic bonds"
- Next in thread: Axel Kohlmeyer: "Re: Problem with psfgen"
- Reply: Axel Kohlmeyer: "Re: Problem with psfgen"
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