From: Axel Kohlmeyer (
Date: Tue May 06 2008 - 13:25:34 CDT

On Tue, 6 May 2008, Alejandro Ortega wrote:

AO> Hi,


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.


AO> I'm using this command, but it only writes the solvation box:
AO> set sel [atomselect top "all"]
AO> $sel writepdb mypdb.pdb
AO> Cheers,
AO> Alejandro Ortega
AO> University of Texas at El Paso.

Axel Kohlmeyer
   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.