From: Peter Jones (p.m.jones_at_optusnet.com.au)
Date: Thu Dec 18 2008 - 22:40:53 CST

Hello all,

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

thanks in advance for any help, it would be greatly appreciated,

Peter Jones