[MMTK] Making DCD from a Series of PDB

khinsen at cea.fr khinsen at cea.fr
Mon Aug 29 09:28:20 CEST 2005


Begin forwarded message:

> The attached message has been automatically discarded.

Another occasion to remind list subscribers that they can only post  
from e-mail addresses that are subscribed to the MMTK list. Otherwise  
posts are discarded with the only copy sent to me, and that one has a  
good chance to be thrown out by my spam filter.... This one was lucky.

> From: Meir Hasbani <mhasbani at princeton.edu>
> Date: 26. August 2005 22:44:21 MESZ
> To: mmtk at python.net
> Subject: Making DCD from a Series of PDB
>
> Hi,
>
> I have a program that models RNA and DNA and produces a series of PDB  
> files. I'd like to convert these pdb's into a dcd trajectory, so that  
> I can view it as an animation in VMD. I've been trying to use MMTK to  
> load each PDB into a universe, take a snapshot, and repeat until I  
> have a Trajectory file, which I then convert to dcd.

If animation in VMD is all you are looking for, a VMD script that loads  
the PDB files in sequence is probably a simpler solution.

> I havent been successful at all. I've attatched one of my original PDB  
> files (file001.pdb), and, an output PDB that MMTK generated (sim.pdb).  
> I've created atoms and molecules for the database, too.
> Below is the code i wrote (I wasn't able to get  
> PDBConfiguration.createMolecules() to work for me). Any suggestions?

Did you try PDBConfiguration.createAll()? It will create AtomCluster  
objects whenever it doesn't have enough information for making Molecule  
objects, but for visualization they are good enough.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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