AMBER Archive (2005)

Subject: Re: AMBER: RESP charges of RNA nucleotides with 3' and 5' ends

From: Qing Zhang (qingzhang_nyu_at_yahoo.com)
Date: Thu Jul 07 2005 - 19:48:40 CDT

> --- Ilyas Yildirim <yildirim_at_pas.rochester.edu>
wrote:
>
> Dear Qing Zhang,
>
> Thank you very much for your answers. It answered
> all of the questions I
> needed to know.:) The only thing that still bugs my
> mind is the 8th and
> 9th parts of the resp program (or maybe I am
> confused a little bit). Is
> the 7th part the charge constraints when the atoms
> are within the
> molecule? For instace, when nmol=1, there can be
> charge constraints in
> the molecule. When nmol=2 (or more), the constraints
> can be between 2-3
> molecules (which means intermolecular).

You're right.

> So, I would
> guess that in your
> sample the constraints are intermolecular (which
> means the 8th and 9th
> areas are used).

I just looked at the RESP manual and the sample. There
is one blank line after the 6th area in the sample,
which means the 7th area (intramolecular charge
constrain) is not used but the 8th area
(intermolecular charge constraints) is used. The both
have the format of

ngrp (I5), grpchg (F10.5)
imol, iatom (16I5)

The above two lines are for one constraint. In the
sample, there are two constraints (for DX), which
occupy 4 lines.

The 9th area is not used in the sample because we do
not use multiple molecule atom equivalencing, which is
used to equivalence some backbone atoms between A, T,
G, C in the force field development. This area has a
format of

ngrp (I5)
imol, iatom (16I5)

For more examples, you can look into the RESP sample
directory in AMBER (at least in version 6 and 7):
  examples/resp_charge_fit/

Sincerely,

Qing

======================================
Qing Zhang, Ph.D.
Research Associate
Molecular Graphics Laboratory
Department of Molecular Biology, MB-5
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000
Tel: (858) 784-2202
Fax: (858) 784-2860
Email: qzhang_at_scripps.edu
======================================

                
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