Thanks very much Ray. Very helpful. crystal waters were read in without problems.
Is it saying that all-atom and united-atom forcefields in Amber treat TIP3 water the same way?
Lee
________________________________________
From: owner-amber.scripps.edu [owner-amber.scripps.edu] On Behalf Of Ray Luo [rluo.uci.edu]
Sent: Thursday, October 25, 2007 2:20 PM
To: amber.scripps.edu
Subject: RE: AMBER: Including crystal water when using united-atom forcefield leaprc.ff03ua
Lee,
Before loading your pdb file, load the ion and solvent libraries first as
follows:
loadOff ions94.lib
loadOff solvents.lib
HOH = TP3
TIP3 = TP3
WAT = TP3
All the best,
Ray
==========================================
Ray Luo, Ph.D.
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900
Phone: (949) 824-9528
Email: rluo.uci.edu
Web: http://rayl0.bio.uci.edu/
==========================================
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Yang, Lee-Wei
Sent: Thursday, October 25, 2007 7:46 AM
To: amber.scripps.edu
Subject: AMBER: Including crystal water when using united-atom forcefield
leaprc.ff03ua
Dear all,
I may miss something very basic here. Is there a water model for united-atom
force field such as leaprc.ff03ua?
'HOH' or 'WAT' in the PDB file can not be read in by leap when 'source
leaprc.ff03ua'.
I wonder how people include the crystal waters when using united atom force
field in AMBER?
(I have to use united atom force field for the deoxy-state of my molecule as
suggested in
............./amber/amber9_patch34/dat/contrib/heme/0README)
Regards,
Lee
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Received on Sun Oct 28 2007 - 06:07:30 PDT
