Re: AMBER: Some questions in building a new residue

From: Chung-Chien Wei <>
Date: Thu, 11 Mar 2004 03:49:33 +0800

Dear Amber Community,

In Prof. Duan's work "A Point-Charge Force Field for Molecular Mechanics
Simulations of Protein Based on Condensed-Phase Quantum Mechanical
Calculations", on J. Comput. Chem., the section "Charge Derivation" wrote:

"Effective charges were obtained by fitting the electrostatic potential of
peptides, using RESP method. A two-stage fitting procedure was used.
(1)In the first stage of fitting, the two conformers (alpha & beta) of each
dipeptide (ex:Ace-Ala-Nme) were combined.
(2)In the second stage, the chemically equivalent atoms were set to hove the
same charges, while the charges of the terminal blocking groups and those of
heavy atoms were fixed. Because the charge-marching process may introduce
small errors, we purposely limited the errors to the matched atoms by fixing
the charges of the blocking groups and heavy atoms.
(3)Finally, the charges of the blocking group were fit by combining
electrostatic potentials of all amino acids."

Now I have some questions:
Question 1 is about step(1) that how to "combine" the two conformers ? (just
averaging phi & psi angles ?) Is it just to get single conformation ?
Question 2 is about step(3) that if you use dipeptide (Ace-Ala-Nme) to run,
how do you remove charge of Ace & Nme and retain the charge of Ala part zero
? (Because charge of Ala in AMBER library without Ace & Nme is zero, and not

So I hope that someone can instruct me explicit steps for building a new
residue well.

Thank you a lot !


Chung-Chien Wei

----- Original Message -----
From: "Ilyas Yildirim" <>
To: <>
Sent: Thursday, March 11, 2004 2:57 AM
Subject: Re: AMBER: Some questions in building a new residue

> Dear Wei,
> I have come to the same problem too. I am trying to recalculate the RESP
> charges for Cytosine molecule which was originally done by Cornell et all
> 95 paper. They have the RESP charges for Cytosine for different sugars
> attached to the base. As far as I understood from the scripps' website,
> they are using the
> #P mp2/6-31g*
> basis set. And the results are done for this space.
> But in the RESP Help page of scripps, they suggest to use hf/6-31g* with
> Iop(6/33=2) command function in the gaussian.
> The main problem for all of us, I think, is the initial unoptimized
> structure of the molecule. There can be a lot of conformations for a
> specific molecule, and depending on which conformation you choose, the
> resultant RESP charges will be different. For cytosine molecule, it is
> easy to find the initial structure, but if someone wants to do the
> calculations for a structure which does not have an explicit crystal
> structure in the databases, this will be a problem.
> Best,
> --
> Ilyas Yildirim
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Received on Wed Mar 10 2004 - 19:53:01 PST
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