From: Axel Kohlmeyer (
Date: Fri Dec 19 2008 - 09:56:01 CST

On Fri, 19 Dec 2008, Peter Jones wrote:

PJ> Hello all,
PJ> I have a dcd format CHARMM trajectory from a system that contains an ACE and
PJ> NME capped peptide. I wish to convert the trajectory to AMBER crd format
PJ> which I have tried with both ptraj and catdcd but when visualised in VMD
PJ> with the AMBER topology file, the caps are not right. I suppose this is to
PJ> do with the different ways the cap atoms are handled. I wonder if anyone
PJ> knows of a solution to this problem?


please note that neither the dcd nor the crd file format have any
information about the topology or identidy of the atoms, they only
contain lists of coordinates. on visualization now, the identity of
atoms, labels, bonds etc. depends on the corresponding topology file.
so it is most likely that your topology file is inconsistent with
the order of the atoms in the .dcd and .crd file.

vmd and all other codes rely on the user providing proper data files.


PJ> thanks in advance for any help, it would be greatly appreciated,
PJ> Peter Jones

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