Re: [AMBER] Problem in antechamber execution Problem in antechamber execution problem in antechamber execution

From: Daniel Roe <>
Date: Tue, 1 Oct 2013 10:08:48 -0600


On Tue, Oct 1, 2013 at 9:15 AM, Tanmoy Paul <> wrote:
> Dear amber users,
> I am trying RESP charge fitting using
> ANTECHAMBER for HCA2( PDB id: 2CBA). I have used gaussian09 to

It looks like you are trying to parameterize an entire protein using
antechamber, which is the wrong approach. Antechamber is designed for
developing parameters for small ligands, cofactors, building blocks of
larger molecules (e.g. amino acids), etc. Force fields with parameters
for standard amino acids already exist; the correct approach is to use
the 'LEaP' program to load one of these force fields, load your
structure, then write out a topology and restart file which can be
used for MD. I highly recommend you run through a few of the Amber
tutorials (, especially B1, as well as
read chapters 2 and 4 of the AmberTools 13 manual.

Hope this helps,


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Tue Oct 01 2013 - 09:30:07 PDT
Custom Search