AMBER Archive (2006)

Subject: AMBER: System in polarizable waters

From: Martin LEPSIK (
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

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

Looking forward to hearing from you.

Yours sincerely,

Martin Lepsik

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