AMBER Archive (2003)

Subject: Re: AMBER: RESP charges

From: Junmei Wang (JWang_at_encysive.com)
Date: Wed Dec 10 2003 - 17:29:19 CST

In this situation, prepgen can't work properly. You may solve this problem
as the following: generate an ac file from gaussian output file; generate
resp input file with respgen and do modifications (you want to the metal to
bear an integer charge); run resp to get resp charges and read in to the ac
file with antechamber; For each residue, extract the corresponding part
from the ac file (you may ignore the bond connection information) to form a
mpdb file; for each residue, read in the mpdb file and generate the prep
input file with antechamber. This procedure should work for you.

Best

Junmei

===============================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Email: jwang_at_tbc.com
Homepage: http://sigyn.compchem.ucsf.edu/members/jmwang/index.html
===============================================================

                                                                           
             Youyi Peng
             <pengyo_at_UMDNJ.EDU
> To
             Sent by: amber_at_scripps.edu
             owner-amber_at_scrip cc
             ps.edu
                                                                   Subject
                                       Re: AMBER: RESP charges
             12/10/2003 04:48
             PM
                                                                           
                                                                           
             Please respond to
             amber_at_scripps.edu
                                                                           
                                                                           

IN the origonal mol2 file every atom has different name. But after mol2
file
was converted to g98 input gcrt file with antechamber, the same atom has
the
same name. And so does every atom in the g98 output log file. I need to
point
out here is that my system is not a single molecule but a hexacoordination
system including four molecules and a metal ion. Does antechamber apply to
this situation?
Thanks.

Youyi

"David A. Case" wrote:

> On Wed, Dec 10, 2003, Youyi Peng wrote:
>
> > resp.prepi file goes here:
> >
> > 18 H7 h1 E 17 16 13 1.090 108.895 -137.317
0.035
> > 19 H8 h1 E 17 16 13 1.089 108.946 102.607
0.035
> > 20 H9 h1 E 17 16 13 1.090 108.869 -17.363
0.035
> > 21 X 1 0 1 4.337 nan 496.982
0.000
> > 22 X 1 0 1 4.337 nan 496.982
0.000
>
> Are all of your atom names unique? Note that antechamber requires that
> everything be in a single residue, and that no duplicate atom names
appear.
>
> ..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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