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

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Tue, 15 Jun 2010 10:36:18 -0700

> 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 don't know how can I
> add methyl groups to my .pdb file. Output file (.pdb) of
> [],
> nucgen or nab hasn't any hydrogen atom to exchange it with carbon. I don't
> think but can I exchange hydrogen
> atoms with carbon in the output pdb file of LEaP and then again let
> LEaP to add the extra hydrogens?

You have to have residue definitions including the methyls, which
requires charge derivation. See the tutorials for examples of
defining new residues. You must decide what method of charge
derivation is sufficient for your purposes. The residue names must
be different from the standard ones, and must be consistent between
the residue definitions and pdb. In any case you will need to add
your methyl hydrogens in order to calculate the charge. A graphical
editor can be used, e.g. xleap will let you delete and draw in what
you need and then select the atoms and energy minimize in leap to
clean up the methyl group coords.


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Received on Tue Jun 15 2010 - 11:00:18 PDT
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