[AMBER-Developers] [romain.wolf.gmail.com: Re: Amber atom type naming (and parms)]

From: case <case.biomaps.rutgers.edu>
Date: Sat, 17 Dec 2011 10:33:37 -0500

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 better?
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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