AMBER Archive (2003)

Subject: AMBER: RESP charge

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Mon Nov 17 2003 - 08:46:32 CST

Hi Dr Case,
  In a old poster 2002, you recommended a simple procedure to calculate
RESP charges. This poster is followed. Now I also want to calculate RESP
charges for a system consisting of several fragments which includes a Mg
ion. I wonder if I can use this simple procedure to do the calculation or I
have to go the traditional method. It seems antechamber doesn't recognize
Mg.
Thanks in advance.

Youyi Peng

The old poster goes here.

On Tue, Apr 23, 2002, Michael G Cooney wrote:

> I was just wondering if anyone knew of a good tutorial for the RESP
> charge-fitting program.

The antechamber program (in version 7) can help you create your own
tutorials to study (or to avoid having to learn the details of resp
input at all.....).

Try this:

    antechamber -i name.pdb -fi pdb -o name.com -fo gcart

will create "name.com" that can be fed to Gaussian, e.g.

    g98 < name.com > name.log

Now, you can use antechamber to automatically run the first and second
stage RESP:

    antechamber -i name.log -fi gout -o name.prepi -fo prepi \
          -c resp -s 2

This will create the required resp input files for your molecule (they
will be called ANTECHAMBER_RESP1.IN and ANTECHAMBER_RESP2.IN), and you
can study the output files as well (ANTECHAMBER_RESP1.OUT and
ANTECHAMBER_RESP2.OUT). The resp charges will end up in the "name.prepi"
file, which can be loaded into LEaP.

...hope this helps....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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