Hi,
On Thu, Sep 17, 2009 at 01:02:18PM -0400, case wrote:
> On Thu, Sep 17, 2009, Scott Brozell wrote:
> >
> > ACML has BLAS, but not CBLAS according to what I heard.
>
> BLAS and CBLAS are the same thing, just implementations of the BLAS API using
> different languages. So, there would not be any need to combine ACML and
> CBLAS.
No, they have the same functionality, but different API's.
The difference is in the names:
Each CBLAS function's name is the BLAS name with cblas_ prepended.
MKL defines these, eg:
/usr/local/intel/mkl/10.0.3.020/lib/em64t/libmkl_intel_ilp64.a:cblas_saxpy.o:0000000000000000 T cblas_saxpy
but ACML does not.
I see now that sff uses a cblas where
each function's name is the BLAS name with _ postpended.
Both have those.
/usr/local/intel/mkl/10.0.3.020/lib/em64t/libmkl_gf_ilp64.a:_saxpy.o:0000000000000000 T saxpy_
/usr/local/acml-4.0.1/pgi64_mp_int64/lib/libacml_mp.so:00000000014de8a0 T saxpy_
I see now that netlib's cblas is just an f2c of their blas.
Sorry that didn't register last night.
This looks like a hack. Why add a trailing underscore if u have
converted via f2c. Isn't this asking for trouble with fortran
mangled names which can add a trailing underscore among other mangles.
> > The idea behind sff was the nab-language-less stuff of nab that
> > might be useful to other programs. So there's some probably small
> > gain by keeping it to one programming language.
>
> I agree.
>
> > With Chimera and the Amber score prep changes in 6.3 one can avoid mopac
> > in DOCK per se.
>
> How does this work? That is, how are the ligand charges calculated?
On Thu, Sep 17, 2009 at 10:34:47AM -0700, Eric Pettersen wrote:
>
> In Chimera, Antechamber is called which in turn calls mopac.
And Antechamber and mopac are distributed with Chimera.
Then use the -c option in prepare_*amber.pl
Usage: $0 [-c] [-i] DOCK_ranked_mol2_file Receptor_PDB_file
...
-c
Use charges from the DOCK_ranked_mol2_file.
The default behavior is to generate AM1-BCC charges.
This option must occur before DOCK_ranked_mol2_file.
After more use with dock, we clearly got the default wrong in amber score
prep.
scott
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Received on Thu Sep 17 2009 - 12:30:02 PDT
