AMBER Archive (2003)

Subject: RE: leap remove command

From: Yong Duan (yduan_at_udel.edu)
Date: Mon Mar 17 2003 - 06:32:21 CST

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_at_morita.chem.sunysb.edu]
Sent: Monday, March 17, 2003 12:31 AM
To: amber_at_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