AMBER: Re: using RESP

From: Ilyas Yildirim <>
Date: Tue, 25 Sep 2007 19:04:52 -0400 (EDT)

Dear Edoardo,

I am not sure what is the best way to attack your system, but the resp
protocol is very straigthforward. You create a structure (let's say a
.pdb file), optimize it using gaussian, and then calculate the MEP points
using gaussian. After that, you create the resp input files, and that is

In order to create a gaussian input file for the system, there is an easy
way, done using antechamber:

antechamber -i ***.pdb -fi pdb -o ***.gcrt -fo gcrt

This will create a gaussian input file which will optimize the structure
and calculate the MEP points. The problem for your system is that you have
an CU in it. I am not a gaussian expert, but there are papers in the
literature, which talks about how/what to chose for the basis set for
CU. Your main problem will be this (I think). People in this mailing list
might have some experience on CU.

There is also a program, called R.E.D., which is the automated version of
the resp protocol. Francois can be more helpful on this.

Even though RESP protol is straigthforward, creating the resp input files
can be a hassle. You might want to check out your $AMBERHOME directory:


You will see some examples here, which can help you to understand the
input files.

My suggestion would be (if you want to follow the resp protocol), read the
literature and decide which basis set is good for CU in your system.
Create your complex (3CYG+Cu), and use the specific basis set just
to CU, and 6-31G* basis set to the rest of the atoms. Optimize it. Then,
calculate the MEP points for this optimized structure (using gaussian).
Create your resp input files (I would suggest you to constrain the
terminal charges to the ones seen in the AMBER force field). Run resp and
get the charges.

This might look a little bit hard, but once you understand gaussian/resp,
it will look straigthforward. Maybe someone else might have a better way
to attack to your system.

Good luck,

PS: It is better to post your questions to the AMBER mailing list, as
people can be more helpful.

On Tue, 25 Sep 2007 wrote:

> Hi, Thanks for advice!
> Have you experience in using RESP?
> I do not have any experince with this utility; I look around on amber
> reflector bit I'm still very confused.
> Do u have any good strating point?
> Thanks
> Edoardo

  Ilyas Yildirim
  = Department of Chemistry      -                              =
  = University of Rochester      -                              =
  = Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) =
  =                     =
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Received on Wed Sep 26 2007 - 06:07:26 PDT
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