Yes, in principle, you can edit the topology file. But if the parameters
of those extra water molecules are in the topology file, removal of them
could be a little tedious. Good luck.
yong
-----Original Message-----
From: CUI, Guanglei [mailto:cuigl.morita.chem.sunysb.edu]
Sent: Monday, March 17, 2003 12:31 AM
To: amber.heimdal.compchem.ucsf.edu
Subject: RE: leap remove command
Dear all,
Thank Darden and Duan for answering my question. After diff the two
topology files I have, I found it's something else, not the solvent.
remove command in leap seems to work correctly. The IFBOX > 0 part
from the two topology files are identical. I think one can manually
edit this section of the topology file to fix the number of solvent,
like in creating belly topology when having a multimolecular solute,
for example double strand DNA. Am I right?
--
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790
Received on Mon Mar 17 2003 - 12:53:02 PST
