Re: [AMBER-Developers] [ Re: Amber atom type naming (and parms)]

From: Yong Duan <>
Date: Sat, 17 Dec 2011 10:02:32 -0800


Indeed, it's very challenging and impossible to cover all possible
fragments. In addition, we also face the challenge of a robust
sub-structure search tool.

What if the goal is to make a database of a subset of fragments that are
most commonly used or difficult to parameterize? Is a database of hundred
fragments useful?

Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
On 12/17/11 7:33 AM, "case" <> wrote:
>At Romain's request, I am forwarding parts of a recent email about force
>----- Forwarded message from "Romain M. Wolf"  -----
>Subject: Re: [AMBER-Developers] Amber atom type naming (and parms)
>From: "Romain M. Wolf"
>Date: Thu, 15 Dec 2011 21:44:24 +0100
>A remark regarding atom types and the idea to use fragments for organic
>molecules.  My advice: DON'T!
>Working in an environment where small molecules are as important as
>proteins or RNA/DNA, I must warn that the number of required fragments
>exceeds anything most people imagine.
>Regarding partial charges in small organics: the current 'fast' AM1-BCC
>method is not bad at all. A correction for symmetry would probably be
>a decent amendment (e.g., a methyl group should always have 3 Hs with
>identical partial charges). But despite this shortcoming, the charges
>themselves are very reasonable (and FAST to compute). I do not see how
>pre-computed partial charges would be incorporated into MANY thousands of
>required fragments.
>[Junmei (or anyone): could we think about symmetrizing am1-bcc charges
>I think the code does some of this, but doesn't recognize methyls, etc.]
>I have seen a few suggestions to generate comprehensive tables for
>all atom types in all Amber FFs. This is an excellent idea. These
>tables should be part of the documentation and not just be found in the
>parameter files. Also, definitions should be commented, by examples if
>necessary. Having ten definitions of carbon atoms in the style "Csp2 in a
>ring" would not be of much help. And of course the occurrence of the type
>(which FFs it is used in) should be mentioned.
>----- End forwarded message -----
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