Subject: AMBER parameter database

From: "Dr Richard Bryce" <[email-masked]>
Date: Fri, 29 Jun 2001 17:07:30 GMT

I would like to announce to computational chemists using AMBER 
the creation of an AMBER parameter database service. I've already 
compiled a limited number of published AMBER parameters for 
some molecules and residues - including the cofactor, FMN and a 
nucleotide-sugar, GDP- mannose.  These are available for users to 
download. The URL is   

pharmacy.man.ac.uk/amber  

In addition to OFF/PREP, FRCFLD/FRCMOD files, and information 
about the developers (name/website/etc.), a literature reference is 
also provided with the parameters to stress that these parameters 
should be used carefully.  However, it is anticipated that the 
archived files will provide a useful starting point for other studies 
and parametrization of similar molecules.   

Only a very basic selection of molecules are currently contained by 
the database.  For the service to be of most benefit, it would be 
really useful if groups who have developed parameters could submit 
these parameters to the database (by emailing me at 
[email-masked]), providing a PREP or OFF file, FRCMOD or 
FRCFLD file, a literature reference and information about 
themselves.   

Examples of parameters that would be useful to add to the 
database include special residue types, such as anionic cysteine, 
or selenocysteine, unusual nucleic acids, organic compounds, 
drug-like molecules with functionality not already covered by the 
standard Cornell et al. parm9x.dat force field.   

I hope this service will be of use to people, and would appreciate 
your comments and suggestions.   

Richard 

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 Richard A. Bryce                  
 School of Pharmacy and Pharmaceutical Sciences, 
 University of Manchester, Manchester, M13 9PL, U.K. 
 Tel:(+44) (0)161 275 8345 Fax: (+44) (0)161 275 2481
 http://pharmacy.man.ac.uk/rab
 [email-masked]     
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