From: Yarrow Madrona (
Date: Mon Apr 08 2013 - 18:42:49 CDT


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

Thank you

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