AMBER Archive (2002)

Subject: Re: amber7 and tip5p

From: David Case (case_at_scripps.edu)
Date: Wed Apr 24 2002 - 16:04:05 CDT

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

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

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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