Dear Robert,
I had the same problem before, and there is a simple
solution in the documentation, much simpler than what
I have done before ;)
use the nobox option in ptraj not to dump the box info
(I guess you use a periodic box) which is treated as
atomic coordinates in VMD. Your prmtop should be fine.
I hope this helps,
Peter Varnai
Received on Wed Apr 04 2001 - 01:44:26 PDT
