Re: Graphene pdb/psf files cannot be read by psfgen

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. Kind regards, wanzhi ________________________________ 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: readpsf graphene.psf coordpdb graphene.pdb then you add other molecules readpsf smth.psf coordpdb smth.pdb and output the final structure writepsf final.psf writepdb final.pdb a more detailed explanation is provided in the psfgen user guide, available in the website. Regards; Eduardo On Feb 15, 2012, at 8:14 AM, Wanzhi Qiu wrote: Dear NAMDers, 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: >coordpdb graphene.pdb 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) >readpsf graphene.psf 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. Many thanks, Wanzhi ----------- Wanzhi Qiu, Ph. D. Senior Researcher National ICT Australia Department of Electrical & Electronic Engineering The University of Melbourne Parkville, Victoria 3010 Australia

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