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

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Wed Feb 15 2012 - 08:11:10 CST

hi Wanzhi,

I also faced the same problem.I created .psf and .pdb files for
graphene.But when we added to some other system by using merge structures
in VMD some coordinates become zero's.The solution which I find for this as
follows

1. After merging the the two structure in VMD I got .psf and .pdb files.
2. I added the two coordinate files with VMD ( manually in the same order
as you gave in merge structures )
3. loaded the .psf file witch you built in VMD (merge structures) and
manually added .pdb in VMD
4.By using save coordinates was gave correct .pdb file for combined
structure.

I Hope It will work for you.But If you find any other solution,Let me know

cheers

subbarao kanchi
physics Dept
IISC Bangalore
INDIA

On Wed, Feb 15, 2012 at 4:36 PM, Cruz-Chu Eduardo Roberto <
eduardo.cruz_at_mavt.ethz.ch> wrote:

> 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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