[Dock-fans] amber-scoring

Francesco Pietra chiendarret at yahoo.com
Wed Sep 12 10:31:38 PDT 2007

As a potential newcomer to DOCK6 (for different purposes than pharma-scoring),
two questions related to problems I am faced with:

(1) Is it any way to use opemmpi for parallelization (that I use for Amber9,
both compiled with Intel) in place of MPICH2? Having limited experience with
such tricks, I foresee major problems for me. In particular if the code is
Fortran, where Intel defeats GNU compilers.

(2) Is it productive to use amber scoring? GB with Amber9 for large systems is
unproductive with respect to explicit solvent-PME. Not to say about all
pitfalls by implicit solvents.

francesco pietra (newcomer to the list, not yet asked to download DOCK)

Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1584
Palazzo Ducale
55100 Lucca, Italy

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