AMBER Archive (2009)

Subject: Re: [AMBER] atom type

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Dec 23 2009 - 07:00:39 CST

Dear Shamoon Ahmad Siddiqui,

> We have a pdb file where the O6-guanine of DNA is connected to a
> methyl group. What will be the atom type for the methyl group
> connected to O atom? Should we determine atom type for all atoms of
> O6-methylguanine by using antechamber or we have to specify only atom
> type for the additional methyl group?

The FF atom type of the O6 atom of guanine is "O" because it belongs
to a carbonyl. In your Methyl-O6-guanine, the atom type of O6 becomes
"OS" because this is an ether.

Other FF atom types should not change...

regards, Francois

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