VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Nov 08 2007 - 21:55:17 CST

On Thu, 8 Nov 2007, Dibyadeep Paul wrote:

DP> Sir, will just merging together two pdb files that work? What I want

why not?

DP> is to have another pdb file, which will be have the two protein
DP> molecules simultaneously, so that I can directly use the single file,
DP> instead of the two files. Wont it also be necessary to modify the
DP> numbering of the atoms and molecules etc? I dont think these can be

no. at least not for visualization purposes. VMD is a visualization
tool and as such (deliberately) has no knowledge of (bio-)chemistry.
thus VMD does not care about the numbers, they are just "labels".

if you want to use the resulting system for setting up a simulation
things are different. but then you would have to split everything
into seperate segments anyways, so that the advance merging would
be a waste of time. please see the NAMD/psfgen documentation or
tutorials for more details.

cheers,
   axel.

DP> achieved by simply using cat.
DP>
DP> Sincerely
DP>
DP> Dibyadeep
DP>
DP> >
DP> > --
DP> > =======================================================================
DP> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
DP> > Center for Molecular Modeling -- University of Pennsylvania
DP> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
DP> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
DP> > =======================================================================
DP> > If you make something idiot-proof, the universe creates a better idiot.
DP> >
DP> 

-- 
=======================================================================
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.