On Fri, 19 May 2017 03:03:15 +0000
MINGREN SHEN <mshen32.wisc.edu> wrote:
> Hi, I have been searching the Internet for a while, and I have
> followed advice from this post
> ( http://archive.ambermd.org/201006/0461.html ) 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.
server.
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.
Cheers,
Hannes.
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Received on Fri May 19 2017 - 01:00:03 PDT
