AMBER Archive (2004)

Subject: Re: AMBER: unnatural base - RESP charges in ANTECHAMBER

From: Junmei Wang (
Date: Mon Jun 07 2004 - 20:22:31 CDT

If you haven't performed gaussian calculations, you may generate a gcrt or
gzmat file and run gaussian (98, 03 etc). You may need to modify the net
charge and 2S+1 if it is necessary. After you get the gaussian output file,
principally you could generate the two-stage resp charge with a command
like "antechamber -fi gout -fo mol2 -i gaussian.out -o molecular.mol2 -c
resp". Of course, you can also generate the resp charge step by step: (1)
extract ESP from gaussian with espgen; (2) generate an ac file from
gaussian output file with antechamber and run respgen to get the resp input
files; (3) run resp to get two-stage resp charges; (3) read in the resp
charge using antechamber with "-c rc -cf qout" flag. Here qout is the
default name of resp charges generated by resp.

Hopefully it helps



Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
=============================================================== wrote on 06/07/2004 07:12:56 PM:

> Hi:
> We'd like to compute RESP charges for an unnatural nucleoside.  We
> know how it works in principle -- the joint between the nucleoside
> and the phosphate -- but we don't know how to setup the input for
> ANTECHAMBER and there does not seem to be an example.  Reading the
> code to figure out the input would be an option; but it would take a
> while and I'd rather not go that way.  So, if there is somebody with
> such an input, we would like to have that template.  That would
> really help us.
> Best, Rainer.
> --
> -------------------------------------------------------------------------
>       "We know accurately only when we know little; with knowledge
>                    doubt increases."  J. W. von Goethe
> -------------------------------------------------------------------------
>          Visit us on the web at
> -------------------------------------------------------------------------
> Dr. Rainer Glaser                                     MM      MM  UU   UU
> Professor in Chemistry      Tel:  (573) 882-0331      MMM    MMM  UU   UU
> Department of Chemistry     Fax:  (573) 882-2754      MMMM  MMMM  UU   UU
> University of Missouri      Home: (573) 445-3094      MM MMMM MM  UU   UU
> Columbia, MO 65211                                    MM  MM  MM  UUUUUUU
> =========================================================================

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to