RE: leap remove command

From: Yong Duan <>
Date: Mon, 17 Mar 2003 07:32:21 -0500

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.


-----Original Message-----
From: CUI, Guanglei []
Sent: Monday, March 17, 2003 12:31 AM
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
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