RE: producing a post-ptraj prmtop

From: Guanglei Cui <>
Date: Tue 3 Apr 2001 21:13:27 -0400

Hi, Robert,
    rdparm, the sister to ptraj, has stripwater function too. You can load
your topology and stripe all the water molecules then save it.


Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook

-----Original Message-----
From: R. M. Fesinmeyer []
Sent: Tuesday, April 03, 2001 8:21 PM
Subject: producing a post-ptraj prmtop

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?

Robert Fesinmeyer
Received on Tue Apr 03 2001 - 18:13:27 PDT
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