Re: [AMBER] How to use Amber GAFF force field for methylated DNA

From: Hannes Loeffler <>
Date: Fri, 19 May 2017 08:36:15 +0100

On Fri, 19 May 2017 03:03:15 +0000
MINGREN SHEN <> wrote:

> Hi, I have been searching the Internet for a while, and I have
> followed advice from this post
> ( ) that I can use PyMoL
> to add


> Since methyl groups is a simple functional group so I think this
> should already be well studied in GAFF.

...and so common that you should probably follow the advice in the last
sentence of that post: look into the literature. It may also be that
suitable parameters are already available on the database of the R.E.D.

Given that a methyl group is a fairly minor modification to a
nucleotide I think it would be best to derive charges consistent with
the original AMBER DNA force field i.e. follow their protocol.

When you use a mol2 file with antechamber make sure that it has the
BOND section properly set up.


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Received on Fri May 19 2017 - 01:00:03 PDT
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