VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Thu Sep 04 2014 - 07:09:58 CDT

Looks to me like the most likely problem is that those hydrogens have non-standard names in your input PDB file. When PSFgen hits an atom name it doesn't recognise in a residue, it ignores it. Also as part of its process it adds all missing atoms in each residue using idealized internal coordinates. Put those two together and you'll get the effect you see.

Tristan Croll
Lecturer
Faculty of Science and Technology
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 4 Sep 2014, at 1:19 pm, "Boshra Moradi" <boshra.moradi.1983_at_gmail.com<mailto:boshra.moradi.1983_at_gmail.com>> wrote:

---------- Forwarded message ----------
From: Boshra Moradi <boshra.moradi.1983_at_gmail.com<mailto: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<mailto: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
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