AMBER Archive (2003)

Subject: Re: AMBER: water prep file needed

From: David A. Case (case_at_scripps.edu)
Date: Thu Nov 13 2003 - 15:36:38 CST

On Thu, Nov 13, 2003, Youyi Peng wrote:

> I want to incoorporate one crystal water molecule in my protein. And
> because the oxygen atom of the water molecule forms a coordination bond
> with Mg ion, I want to modify the atomic charges in the coordination
> system in order to accurately model the electrostatic interactions. So I
> need the prep (or .in) and frcmod files for all involved residues. But I
> couldn't find the prep or .in file for water molecule in any directory
> of AMBER7. Anybody knows where to find it or how to make it? Thanks a
> lot.

Various water models are in amber7/dat/leap/lib/solvents.lib. You could
copy one of these to a new name, then modify the charges.

Or, you could use the "edit" command in LEaP to modify an existing water
model, then save it (use saveOff) to a new name.

..good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
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