AMBER Archive (2004)

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

From: Junmei Wang (JWang_at_encysive.com)
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

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
===============================================================

owner-amber_at_scripps.edu 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.
>
> --
>
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