VMD-L Mailing List

From: Boshra Moradi (boshra.moradi.1983_at_gmail.com)
Date: Wed Sep 03 2014 - 21:13:08 CDT

---------- Forwarded message ----------
From: Boshra Moradi <boshra.moradi.1983_at_gmail.com>
Date: Tue, Sep 2, 2014 at 12:59 PM
Subject: fixed atoms_creating psf with out change in pdb
To: vmd-l_at_ks.uiuc.edu

Hi,
I should run a simulation of fixed protein in a box of water. I
took the pdb of this protein from QM calculations in gas phase, and I
should gain the pdb of this protein in solution phase in the
condition that the coordination of atoms in the protein was fixed.
But I find that the coordination of some atoms "like H" during the
creating of psf file,have changed. In "coordpdb part", there are these
warnings:

psfgen) reading coordinates from pdb file 1AMC-PM6-DH2.pdb for segment U
psfgen) Warning: failed to set coordinate for atom H1 ASP:1 U
psfgen) Warning: failed to set coordinate for atom H2 ASP:1 U
psfgen) Warning: failed to set coordinate for atom H ALA:2 U
psfgen) Warning: failed to set coordinate for atom H GLU:3 U
psfgen) Warning: failed to set coordinate for atom H PHE:4 U
psfgen) Warning: failed to set coordinate for atom H ARG:5 U
psfgen) Warning: failed to set coordinate for atom H HIS:6 U
psfgen) Warning: failed to set coordinate for atom H ASP:7 U
psfgen) Warning: failed to set coordinate for atom H SER:8 U
psfgen) Warning: failed to set coordinate for atom H SER:8 U
psfgen) Warning: failed to set coordinate for atom H GLY:9 U
psfgen) Warning: failed to set coordinate for atom H TYR:10 U
psfgen) Warning: failed to set coordinate for atom H GLU:11 U
psfgen) Warning: failed to set coordinate for atom H VAL:12 U
psfgen) Warning: failed to set coordinate for atom H HIS:13 U
psfgen) Warning: failed to set coordinate for atom H HIS:14 U
psfgen) Warning: failed to set coordinate for atom H GLN:15 U
psfgen) Warning: failed to set coordinate for atom H LYS:16 U
psfgen) Warning: failed to set coordinate for atom H LEU:17 U
psfgen) Warning: failed to set coordinate for atom H VAL:18 U
psfgen) Warning: failed to set coordinate for atom H PHE:19 U
psfgen) Warning: failed to set coordinate for atom H PHE:20 U
psfgen) Warning: failed to set coordinate for atom H ALA:21 U
psfgen) Warning: failed to set coordinate for atom H GLU:22 U
psfgen) Warning: failed to set coordinate for atom H ASP:23 U
psfgen) Warning: failed to set coordinate for atom H VAL:24 U
psfgen) Warning: failed to set coordinate for atom H GLY:25 U
psfgen) Warning: failed to set coordinate for atom H SER:26 U
psfgen) Warning: failed to set coordinate for atom H SER:26 U
psfgen) Warning: failed to set coordinate for atom H ASN:27 U
psfgen) Warning: failed to set coordinate for atom OXT LYS:28 U
psfgen) Warning: failed to set coordinate for atom O LYS:28 U
psfgen) Warning: failed to set coordinate for atom H LYS:28 U
psfgen) Warning: failed to set coordinate for atom H LYS:28 U
In the "guesscoord part" there would be new co-ordinations for these
atoms and therefore in "writepdb part", I have a pdb file that the
co-ordinations of atoms in this new pdb against the pdb that I took
from QM calculations, was changed.
this is undesirable. How can I do to solve this problem?
"The co-ordinations of all atoms of protein should be fixed during of
creating psf file"

Thanks in advance