VMD-L Mailing List

From: peter.schmidtke_at_fr.netgrs.com
Date: Tue Apr 09 2013 - 01:12:20 CDT

Hey,

Consider using ambertools ptraj for instance, which could do the pdb export.

Best regards.

Peter

-----Message d'origine-----
De : owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] De la part de Yarrow Madrona
Envoyé : mardi 9 avril 2013 01:43
À : VMD mailing list
Objet : Re: vmd-l: how to convert dcd to pdbs in command line

Hello,

I am trying to convert a dcd to a series of pdb's without opening the VMD GUI. The reason is that I don't have enough ram to store the DCD (70,000
frames) into memory. VMD always crashes unless I use a truncated DCD. I would like to use all frames since the frames will be analyzed by another software (Caver3.0). Is there a way to tell vmd to write out all PDBs in the command line (preferably without water although I can remove those later)?

Thank you 

--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697