Date: Wed, 24 Apr 2002 14:04:05 -0700
From: David Case
Subject: Re: amber7 and tip5p

On Wed, Apr 24, 2002, Sarah Tschampel wrote:
>
> I am trying to create the equivalent of a WAT216 box of tip3p with tip5p.

> Error in numextra_test

You don't say what you did to create the wat216 box. The error message
above is very simple: the prmtop file has a value for NUMEXTRA (at the
top of the file) that doesn't match the number of atoms of type "EP".

Here's how I would do this:

1. make a pdb file of a box of water: (or get your initial coords by
some other mechanism....)

tleap
source leaprc.ff02EP
savePdb WATBOX216 wat216.pdb
quit

2. set up the tip5p model, and use the coords from wat216.pdb (the extra
point positions will be automatically built in):

tleap
source leaprc.ff02EP
WAT = TP5
loadAmberParams frcmod.tip5p
x = loadPdb wat216.pdb
setBox x centers
saveAmberParm x prmtop prmcrd
quit


Then you should have a self-consistent prmtop file.

...good luck...dac