Re: amber7 and tip5p

From: David Case <>
Date: Wed 24 Apr 2002 14:04:05 -0700

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....)

         source leaprc.ff02EP
         savePdb WATBOX216 wat216.pdb

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

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

Then you should have a self-consistent prmtop file.

...good luck...dac

p.s.: please send amber questions to <>, not
to me personally. Many other people can help you out if you do that.

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Wed Apr 24 2002 - 14:04:05 PDT
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