From: Wanzhi Qiu (wanzhiqiu128_at_yahoo.com)
Date: Wed Feb 15 2012 - 20:06:01 CST
Hi Eduardo and All,
Thanks for your reply. Yes you are right psf should be read before reading pdb. Unfortunately this doesn't solve the problem. Same error messages are still returned when issuing readpsf/coordpdb commands from Tkconsole. The psf/psb files have no problem in being loaded to VMD via "mol load" command.
I guess there might be some formatting issues in the psf/pdb files generated this way - starting with the Carbon Nanostructure Builder, then select all, then issue "$all writepdb/psf" commands.
Could you please enlighten me on what might be wrong here.
From: Cruz-Chu Eduardo Roberto <eduardo.cruz_at_mavt.ethz.ch>
To: Wanzhi Qiu <wanzhiqiu128_at_yahoo.com>
Cc: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Sent: Wednesday, 15 February 2012 10:06 PM
Subject: Re: namd-l: Graphene pdb/psf files cannot be read by psfgen
readpsf command must go before coordpdb; that is:
then you add other molecules
and output the final structure
a more detailed explanation is provided in the psfgen user guide, available in the website.
On Feb 15, 2012, at 8:14 AM, Wanzhi Qiu wrote:
I constructed a small graphene sheet using VMD Carbon Nanostructure Builder with options of Bonds, Angles etc are ticked. The result is shown on VMD OpenGL window and pdb/psf files are then generated using writepdb/writepsf commands in Tk console. The files appear to be correct with numbers for bonds, angles etc in the psf file. However, they fail when I try to combine the graphene with other molecules.
The problem is that the generated graphene.pdb/graphene.psf cannot be read by psfgen. In particular, the commands issued in the Tk console and error messages are:
gives following result:
psfgen) reading coordinates from pdb file graphene.pdb
psfgen) no segment
psfgen) Warning: failed to set coordinate for atom C GRA:1
(patten repeat for all atoms)
gives following result:
psfgen) reading structure from psf file graphene.psf
psfgen) error reading atoms
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
I suspect that the problem might be related to the residue name "GRA" in the pdb file. The first 3 lines of the pdb file are:
CRYST1 8.508 7.368 100.000 90.00 90.00 90.00 P 1 1
ATOM 1 C GRA X 1 0.000 0.000 0.000 0.00 0.00 C
ATOM 2 C GRA X 2 -0.709 1.228 0.000 0.00 0.00 C
Please let me know if you have any advices/comments/suggestions.
Wanzhi Qiu, Ph. D.
National ICT Australia
Department of Electrical & Electronic Engineering
The University of Melbourne Parkville, Victoria 3010 Australia
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