From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 05 2007 - 20:09:49 CDT

On Tue, 5 Jun 2007, Arneh Babakhani wrote:

AB> Hi Axel, yes, I was referring to 'molecule' in the VMD sense, I'm aware
AB> of this. I was wondering if there was a way to do this, without merging

no. the h-bond searching uses a grid search which only
works for a single molecule.

AB> the files (because I have a lot of structures, and this might become
AB> cumbersome).

you can try to script/automate the merging. essentially you can create
are new dummy molecule that has no bond/atom information, but the right
number of atoms, then copy over the structure/atom/residue information
etc and process it. i have worked on some scripts to do apply bond and
atom information to atoms with an index offset for some 'selective
molecule loading' plugin for extra large systems (i.e. if you want to
strip off waters from a trajectory on loading). if that would be of
some help for you, give me a holler, and i'll try to dig them out
(the project itself is currently on hiatus, due to too many other
ongoing projects).

cheers,
   axel.

AB>
AB> But, if that's the way I have to do it, then so be it . . . thanks,
AB>
AB> Arneh
AB>
AB>
AB>

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