AMBER Archive (2005)

Subject: RE: AMBER: H-atom types attached to a carbon atom next to carbonyl group

From: Vineet Pande (pande_vineet_at_hotmail.com)
Date: Mon Jan 17 2005 - 14:32:37 CST

>I'm now trying to parameterize a ester compound.
>I would like to ask you how to set the amber atom types of hydrogen that is
>attached to a carbon atom next to carbonyl group. I can not decide whether
>it is HC or H1.

In my opinion, determining Atom types can be sometimes a matter of choice
>> you may try ANTECHAMBER, trust its decision for a while :) and see if
the overall structure looks okay after minimization. The atom types would
mainly dictate hybridization state and local geometries >> main things would
be charges, besides the way impropers are defined and of course torsions
being replicated by those atom types!! Why don't you give GAFF (general
amber force field) and ANTECHAMBER a try for your molecule...
Cheers,
Vineet.

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