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Date: Mon, 17 Jul 2000 15:45:20 -0500
From: Matthew Lee <mlee@adrik.bchs.uh.edu>
Subject: Need help with the prepare module
To: NWChem help <nwchem-users@emsl.pnl.gov>
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Hi,

I am trying to start an MD simulation and I have this question about the
prepare module.  In the maual, it says that the prepare module will
automatically add counter ions and missing hydrogens to the original PDB.  I
used the following input file to solvate my system, but afterwards, I cannot
find any counter ion in the output pdb.  Does NWChem keep track of the
counter ion internally or did I do something wrong?

Thanks.

================================================
title; solvation and hydrogen addition of HIV-1 IN double mutatnt

memory heap 1 mb stack 40 mb global 20 mb
start double

prepare
 system double_em
 modify sequence 59:HIE
 grid 70 1.0
 orient
 center
 periodic
 solvate cube 7.2
 expand 0.10
 touch 0.26
 write rst doubleH_em.rst
 write pdb doubleHOH.pdb
end

task prepare
======================================================
===========================================
--@_@--    Matthew Lee
     V

Graduate Research Assistant
Department of Biochemical & Biophysical Sciences
University of Houston
(713) 743-8367
e-mail: mlee@adrik.bchs.uh.edu
http://adrik.bchs.uh.edu/~mlee
===========================================