As there regularly appears to be inquiries on the email reflector
about parameter availability, I would like to offer 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
r.a.bryce_at_man.ac.uk), 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
_______________________________________________________
Richard A. Bryce
School of Pharmacy and
Pharmaceutical Sciences, Tel: (+44) (0)161 275 8345
University of Manchester, Fax: (+44) (0)161 275 2481
Oxford Road, Manchester, Email: R.A.Bryce_at_man.ac.uk
M13 9PL, U.K. WWW: pharmacy.man.ac.uk/rab
_______________________________________________________
______________________________________________________
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
R.A.Bryce_at_man.ac.uk
______________________________________________________
Received on Fri Jun 29 2001 - 09:47:18 PDT
