The substructure search tool would be a must, but would not be sufficient. A major problem would still be the various connection points a single fragment might have. Unlike AAs and nucleotides, some larger ring fragments can have numerous attach points at which atom types would vary depending on the connection. Similar problems for partial charges.
I guess that most users of GAFF in combination with any of the protein FFs start from ready, complete ligand structures (e.g. from x-ray or from docking). So they have the full structure (at best having to add hydrogens when not relying on automatic tools to do so).
---regards---romain
On 17 Dec 2011, at 19:02, Yong Duan wrote:
>
> Thanks!!
>
> 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
> 530-754-7632
>
>
>
>
>
>
> On 12/17/11 7:33 AM, "case" <case.biomaps.rutgers.edu> wrote:
>
>> At Romain's request, I am forwarding parts of a recent email about force
>> fields....dac
>>
>> ----- 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.
>>
>> ---regards---romain
>>
>> ----- End forwarded message -----
>>
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>
>
>
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--------------------------------------------
Dr. Romain M. Wolf
romain.wolf.gmail.com
Tel. +33 6 63 06 94 33
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Received on Sun Dec 18 2011 - 06:00:04 PST
