VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 06 2008 - 13:25:34 CDT
- Next message: zhenlong li: "running vmd as pbs job"
- Previous message: Alejandro Ortega: "Writepdb with Solvation Box"
- In reply to: Alejandro Ortega: "Writepdb with Solvation Box"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
On Tue, 6 May 2008, Alejandro Ortega wrote:
AO> Hi,
alejandro,
AO> I have a problem when I'm trying to make a solvation box and write the pdb
AO> together with my molecule. Is there a way to write a pdb with the solvation
AO> box (PSF) and my molecule together?
well, you didn't say _how_ you generate your solvation box
and where you have your molecule.
merging structures/topologies requires the use of psfgen.
at least this is how the solvate plugin in VMD work.
i suggest you have a closer look at the NAMD/psfgen tutorials
on the VMD/NAMD homepages and take it from there.
cheers,
axel.
AO> I'm using this command, but it only writes the solvation box:
AO>
AO> set sel [atomselect top "all"]
AO> $sel writepdb mypdb.pdb
AO>
AO>
AO> Cheers,
AO> Alejandro Ortega
AO> University of Texas at El Paso.
AO>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
- Next message: zhenlong li: "running vmd as pbs job"
- Previous message: Alejandro Ortega: "Writepdb with Solvation Box"
- In reply to: Alejandro Ortega: "Writepdb with Solvation Box"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]