AMBER Archive (2004)

Subject: Re: AMBER: Some questions in building a new residue

From: Ilyas Yildirim (
Date: Wed Mar 10 2004 - 12:57:11 CST

  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.

  Ilyas Yildirim
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On Thu, 11 Mar 2004, 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 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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