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

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Wed Feb 15 2012 - 21:48:00 CST

Hi wanzhi,

    In my procedure every thing is fine. I thought that You wrote correct
.psf for Graphene.Any way I am telling what I did.
First do the tutorial for Carbon nanotube , which is given in NAMD
tutorials.IN that there is a tcl scripting for creating .psf for cnt.
by using that I Created .psf for graphene. For that I wrote A topology (for
Bonding ) file and .pgn file for graphene by using .pdb file which is
generated in VMD.By using this trick I did.

I think now you may do better.

cheers
subbarao kanchi
physics Dept
IISC Bangalore
INDIA

On Thu, Feb 16, 2012 at 7:42 AM, Wanzhi Qiu <wanzhiqiu128_at_yahoo.com> wrote:

> Hi Subbarao,
>
> Thank you! In my situation the first step outlined in your procedure fails
> - the merge cannot be done due to failure in reading psf/pdb files. I guess
> something is wrong with my graphene pdf/pdb files generated using VMD's
> Carbon Nanostructure Builder. Could you let me know which tool you used to
> generate your graphene pdb/psf files.
>
> Many thanks,
>
> wanzhi
>
>
> ------------------------------
> *From:* kanchi subbarao rao <ksubbu85_at_gmail.com>
> *To:* Cruz-Chu Eduardo Roberto <eduardo.cruz_at_mavt.ethz.ch>
> *Cc:* Wanzhi Qiu <wanzhiqiu128_at_yahoo.com>; "namd-l_at_ks.uiuc.edu" <
> namd-l_at_ks.uiuc.edu>
> *Sent:* Thursday, 16 February 2012 1:11 AM
>
> *Subject:* Re: namd-l: Graphene pdb/psf files cannot be read by psfgen
>
> 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
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:24:45 CST