Dear Dr. Bryce,
during my PhD research I concentrated on MD simulations with AMBER 7 on 
HIV protease and its inhibitors. I would like to contribute parameters 
for all moieties of two clinically used inhibitors, saquinavir (SQV) and
indinavir (IDV).


PREPs: as attachment, P? means standard nomenclature of moieties

FRCMODs: attached in the following e-mail

Citation:

*Lepaík M*, Kr(í~ Z, Havlas Z. Efficiency of a second-generation HIV-1 
protease inhibitor studied by molecular dynamics and calculations of 
absolute binding free energies. *Proteins* 2004;57:279-293.

Comments:

The parameters were taken from gaff force field for use with parm99 
AMBER protein force field. Crystal geometries of PR-bound inhibitors 
were used. Single conformation fitting to HF/6-31G* ESP was applied.


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I would be grateful if you could add these parameters to the AMBER
database.

Yours sincerely,

Martin Lepsik

		 
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Martin Lepsik, Ph.D.
Center for Complex Molecular Systems and Biomolecules,
Institute of Organic Chemistry & Biochemistry, Czech Rep.
Flemingovo nam. 2, 166 10, Praha 6
phone: +420-220 410 318
e-mail:lepsik@uochb.cas.cz