Re: removing water from big dcd files

From: Axel Kohlmeyer (
Date: Wed Mar 04 2009 - 13:49:48 CST

On Wed, 4 Mar 2009, Roman Petrenko wrote:

RP> Carma is an excellent tool, and i don't understand why it is not so popular.

RP> By the way, i had exactly the same problem and used psfgen for the
RP> generation of new psf file.

why psfgen?

$sel writepsf protein.psf

does the trick nicely. you don't need any angle,
dihedral, etc definition for visualization.

but angles & co. are supported in the latest alpha
version of the code. in addition i'm there is an API
and a tcl package to manipulate bond, angle, etc. definitions.

i'm currently working on additional scripts on top of
that to import or export this information from/to external
files, e.g. lammps data files (this is what our group needs).

RP> I guess it would be nice to have one python (or tcl) script which
RP> would call carma to handle dcd file, psfgen to create new psf file.

just write one and send it in.


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

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