VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue May 06 2008 - 13:25:34 CDT

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
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If you make something idiot-proof, the universe creates a better idiot.