Re: [AMBER] MD simulation of methylated DNA: addition of methyl groups to .pdb file

From: case <>
Date: Tue, 15 Jun 2010 14:19:27 -0400

On Tue, Jun 15, 2010, Ehsan Habibi wrote:

> I aim to work on MD simulation of methylated DNA with AMBER 9. Would you
> please give me some information regarding the addition of methyl
> groups to my .pdb file.

I would just use xleap to add the methyl groups, but many other graphical
programs could do this as well. As Bill mentioned, you also need to get a
charge and force field model; antechamber can help here; again other
possibilities exist (check the REDDB database). Do a literature search for
others who have looked at methylated DNA would also be recommended.


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Received on Tue Jun 15 2010 - 11:30:04 PDT
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