Re: AMBER: Some questions in building a new residue

From: Vlad Cojocaru <>
Date: Wed, 10 Mar 2004 18:28:55 +0100

At first glance...the amber charges are calculated with HF/6-31g*. So it
might be that your differences come from the different method that you
use in Gaussian.
I did RESP calculations and they were in agreement with existing data bu
I have never used antechamber. I always used the RESP program so i
cannot say anything about antechamber
Best wishes

Chung-Chien Wei wrote:

> Dear Prof. Duan,
> Sorry to bother you, but I really admire your works on AMBER. I am a
> graduate student in National Taiwan Normal University and now I am
> running a project, whose first step is to create a new residue for
> AMBER. I used Antechamber to do this job and now I have some trouble
> in fitting the atomic charges by RESP. I recalculated the atomic
> charges on Alanine but the results seems to be very different from the
> data in Force Field 94 and your work published on J. Comput. Chem.
> 2003. For example, the atomic partial charges of N atom and alpha-C
> atom on Alanineare -0.405and -0.028 on your calculation,but they are
> -0.863 and +0.177inmy trial (alpha-helix conformation, blocked by ACE
> and NHE). The others are also different by 0.1to 0.2 approximately.
> The results for the beta-conformation is also terrible.
> The ESP is calculated by Gaussian, using B3LYP/cc-PVTZ. Then the file
> is read and calculated by Antechamber with the following command:
> antechamber -i ala_g98.out -fi gout -o ala.prepin -fo prepi -c resp
> -at amber -s 2
> And There is no error message.
> I read the papers discussing RESP and I am not sure if there is
> something I didn't notice. Could you please give me some suggestions
> or some guideness?
> And I really wanna know theappropriate procedure aboutbuilding a new
> or conventional residue.
> Thanks for your kindness.
> Sincerely yours.
> Chung-Chien Wei

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Wed Mar 10 2004 - 17:53:01 PST
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