[AMBER] Questions concerning charges calculated by antechamber

From: Andreas Gavrielides <agavri.hotmail.com>
Date: Mon, 28 Nov 2016 12:36:19 +0000

Dear all,

I try to use the GAFF force field with LAMMPS. I have some problems
considering the charges on the atoms.

To validate the way I use this force field, I try to reproduce some of the calculations presented in paper of Case et al. in J. Comput. Chem. (vol.25, 2004, Development and testing of a general amber force field) on the isolated adenine molecule. I used Antechamber to get the atoms type.

I calculated the charges using two approaches: AM1/BCC using Antechamber and RESP (I did an optimisation at HF/6-31G* level with gaussian and calculated the electrostatic potential at the same level with IOP(6/42)=6 as mentioned in the paper).

Moreover I found charges that could be assigned to the atoms in the gaff.dat file.

My first question is about the charges: The RESP and AM1/BCC charges I calculated are really different (differences can be of 0.60 e) for some atoms (C and N atoms). Is it OK?

Those given in gaff.dat file are all positive. I would like to know how they were computed.

My second question is about the bond, angle and dihedral parameters. Can I use them in the calculations independently the charges chosen? same parameters even if charges calculation scheme is different?

Thanks for your help,

Andreas Gavrielides

Andreas Gavrielides

Doctorant au CIRIMAT-INP Toulouse

SURF Equipe
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Received on Mon Nov 28 2016 - 05:00:03 PST
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