AMBER Archive (2006)

Subject: AMBER: System in polarizable waters

From: Martin LEPSIK (martin.lepsik_at_ibs.fr)
Date: Mon Sep 11 2006 - 11:14:24 CDT

Dear AMBER team,
I have two questions and suggestions regarding the usage of polarizable
waters in AMBER.

First, the order of atoms is different for TIP3PBOX and POL3BOX in
solvents.lib. It is O H1 H2 for the former, while H1 O H2 for the
latter. This results in two water types when adding POL3BOX to several
explicit TIP3P waters. Should I change the order of atoms and/or residue
name WAT-->PL3 of the explicit waters to solve it?

Second, I find it misleading having the default water model in
leaprc.ff02 and .ff02EP TP3 instead of POL3 (although I know about
simulations of polarizable solute in TIP3P water). In order to have
POL3P waters with PL3 names, do I add the 3 lines (shown below) after
loading leaprc, before loading pdb and adding POL3PBOX or differently or
twice??

WAT = PL3
set WAT.1 name "PL3"
loadamberparams frcmod.pol3

Looking forward to hearing from you.

Yours sincerely,

Martin Lepsik

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