[Dock-fans] amber-scoring

Scott Brozell sbrozell at scripps.edu
Thu Sep 13 13:23:31 PDT 2007


Hi,

On Wed, 12 Sep 2007, Francesco Pietra wrote:

> 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.

Yes.  It might be as simple as pointing MPICH_HOME at the Open MPI
installation.  My advice is to use gnu compilers to install
both Open MPI and DOCK.  See the TROUBLESHOOTING section of
DOCK config file install/gnu.parallel for other comments.
This stale thread might be helpful:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-November/000776.html

> (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.

Amber score has been used productively for rescoring;
the computational cost increases as the size of the movable
region increases.  The cost of movable=nothing is similar
to that of the other non-grid based scores.
For a large receptor movable=everything will be slow and
thus may not be productive but still can be useful.
The movable=distance and movable=nab_atom_expression
of Amber score enable detailed control of receptor flexibility.

Many interpretations can be made of the Amber9 benchmarks:
http://amber.scripps.edu/amber9.bench1.html
In general, I won't disagree that explicit solvent-PME is better than
GB for long MD on very large systems, but if you want long large MD
then use Amber not DOCK.  If you want to dock after you have done
long large MD then use DOCK especially if you want to apply a
uniform protocol with some small degree of specific receptor flexibility.

Users with Amber score experience are welcome to comment.
Scott

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



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