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

From: Takashi Nakamura <>
Date: Mon, 17 Jan 2005 18:52:56 +0100

Dear amber mailing list members,

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.
I think carbonyl group can be considered as electron withdrawing group, so
H1 seems better.
But, I'm not sure whether carbonyl group of ester can be considered as
electron-withdrawing substituent or not.
Would you teach me which atom type of hydrogen you select in my case?

I hope someone kindly answer to my question.

Best wishes,
Takashi Nakamura


Takashi Nakamura, Ph.D.
National Centre for Biomolecular Research
Masaryk University, Faculty of Science
  Kotlarska 2, 611 37 Brno, Czech Republic
phone +420-549-49-2558, fax +420-549-49-2556

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Received on Mon Jan 17 2005 - 19:53:01 PST
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