AMBER Archive (2001)

Subject: producing a post-ptraj prmtop

From: R. M. Fesinmeyer (rmf_at_u.washington.edu)
Date: Tue Apr 03 2001 - 19:20:41 CDT

What's a good way to build a new prmtop file after processing a trajectory
with ptraj?

I passed a trajectory coordinate file through ptraj in order to strip the
waters prior to further processing/visualization (I also image'd the system)
. Removing the waters left my peptide and a single Cl- atom. I attempted
to build an appropriate topology file by using ambpdb to generate a pdb file
from the restart file. I then removed the waters (though not the Cl-),
brought the pdb file into tleap, and performed a saveAmberParm to obtain a
new topology file. When I tried to visualize the program with VMD (which
asks for prmtop and mdcrd), the connectivities were not right, giving the
"spider web" effect.

Any suggestions?

Thanks,
Robert Fesinmeyer