From: Fatemesadat Emami (fe2_at_zips.uakron.edu)
Date: Mon Mar 08 2010 - 13:47:43 CST

Hi John,
What if I create .psf files because I have already lammps dcd files obtained
from simulation. Then I have to name my surface elements again. Do you have
any sample of a .psf files for a system including a surface?
Is there any webpage explaining the exact format of a psf file?
Thanks for your time
Fatima
On Mon, Mar 8, 2010 at 11:05 AM, Fatemesadat Emami <fe2_at_zips.uakron.edu>wrote:

> Thank you John
>
>
>
> On Mon, Mar 8, 2010 at 11:04 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>>
>> Hi,
>> If you wish to display a surface in addition to the atoms, you could
>> either have VMD draw the surface with "draw" or "graphics" commands
>> (your program could emit the appropriate commands to a text file that you
>> could then load into VMD), or you could emit the surface as an STL
>> or MSMS file, or another geometric file format that VMD can read.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Mon, Mar 08, 2010 at 10:57:02AM -0500, Fatemesadat Emami wrote:
>> > Thank you very much John,
>> >
>> > Then I won't be able to load my system into vmd from pdb files, is
>> that
>> > right?
>> >
>> > Thank you again,
>> > Fatima
>> >
>> > On Mon, Mar 8, 2010 at 10:25 AM, John Stone <johns_at_ks.uiuc.edu>
>> wrote:
>> >
>> > Hi,
>> > The PDB file format spec is available here:
>> > http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html
>> >
>> > Unless I misunderstand what you mean by "surface", no there is not
>> > a way to represent a polygon mesh or other geometric surface in a
>> > PDB file. PDB files only contain atoms, associated structure data,
>> > and information about the crystallography methods used to determine
>> > the structure, etc.
>> >
>> > Cheers,
>> > John Stone
>> > vmd_at_ks.uiuc.edu
>> >
>> > On Mon, Mar 08, 2010 at 09:59:14AM -0500, Fatemesadat Emami wrote:
>> > > Hi vmd users,
>> > > I am creating pdb files (with my own code) from the Material
>> Studio
>> > > coordinate files. I have a surface in my system that I do not
>> know
>> > how to
>> > > name its elements in the pdb file. I was wondering if anybody
>> can
>> > give me
>> > > an idea of how I have to include a surface in a pdb file or
>> how I
>> > can find
>> > > a sample for such a sys?
>> > > Many Thanks
>> > > Fatima
>> > >
>> > > --
>> > > Yours Sincerely,
>> > > Fateme Sadat Emami
>> > > Nano Scale Laboratory
>> > > Polymer Engineering Department
>> > --
>> > NIH Resource for Macromolecular Modeling and Bioinformatics
>> > Beckman Institute for Advanced Science and Technology
>> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>> >
>> > --
>> > Yours Sincerely,
>> > Fateme Sadat Emami
>> > Nano Scale Laboratory
>> > Polymer Engineering Department
>>
>> --
>> NIH Resource for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>
>
>
>
> --
> Yours Sincerely,
> Fateme Sadat Emami
> Nano Scale Laboratory
> Polymer Engineering Department
>

-- 
Yours Sincerely,
Fateme Sadat Emami
Nano Scale Laboratory
Polymer Engineering Department