AMBER Archive (2004)

Subject: AMBER: Some questions in building a new residue

From: Chung-Chien Wei (
Date: Wed Mar 10 2004 - 11:16:37 CST

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 Alanine are -0.405 and -0.028 on your calculation, but they are -0.863 and +0.177 in my trial (alpha-helix conformation, blocked by ACE and NHE). The others are also different by 0.1 to 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 the appropriate procedure about building a new or conventional residue.

Thanks for your kindness.

Sincerely yours.

Chung-Chien Wei

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