Dear Dave,
attached please find a patch file that relates to the mm_pbsa.pl directory only.
With this:
1.) All data of the examples provided by us until now can be
reproduced after setting dprob=1.6 (and radinc=0.8 in the version from
03.03.2012) explicitly in mm_pbsa_createinput.pm
2.) Examples are adapted according to Qins recommendations:
A) PRBRAD removed from input files
B) Changed mm_pbsa_createinput.pm
IF inp=2: DPROB=1.4, SPROB=0.557
ELSIF PRBRAD set in mm_pbsa.in: SPROB = DPROB = PRBRAD
ELSE SPROB = 1.4, DPROB = 1.4
-> Consistent with Qins recommendations and backward compatible with AMBER11 settings.
C) Changed PRBRAD to SRAD in iAPBS section to ensure consistency with
APBS input and improve clarity -> Adapted mm_pbsa.in of Example 11 accordingly.
D) Removed PRBRAD from required input flags in mm_pbsa_global.pm
All tests for mm_pbsa.pl should pass now.
Many thanks to Nadine Homeyer for making this possible.
Best regards
Holger
On 10.03.12, "David A. Case" wrote:
> I've created a first "release candidate" for Amber12. It comes in two parts:
>
> http://ambermd.org/downloads/AmberTools12.09mar12.bz2
> http://ambermd.org/downloads/Amber12.09mar12.bz2
>
> At least for serial tests, things look pretty good except for some of the
> mmpbsa tests (both perl and python). These may have been caused by very
> recent changes to defaults in pbsa itself. Qin, Jason, Holger and Nadine
> should be looking into these. Testing of the parallel and cuda codes is
> especially encouraged, as are tests with different compilers.
>
> Post your results on the Amber wiki:
>
> http://ambermd.org/pmwiki/pmwiki.php/Main/Amber12Test
>
> Please remember that what users will see are tarballs like those above, and
> *not* what is in the git repo. Be alert for things that are mising from the
> tarballs, or which are present but should not be. The Amber12 file is 40%
> bigger than that for Amber11, so if there are things that don't need to be
> there, please let me know.
>
> ...thx...dac
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Professor fuer Pharmazeutische/Medizinische Chemie
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
Tel.: (+49) 211-81-13662; Fax: (+49) 211-81-13847
Email: gohlke.uni-duesseldorf.de
URL: http://cpclab.uni-duesseldorf.de
++++++++++++++++++++++++++++++++++++++++++++++++++
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Received on Sat Mar 10 2012 - 09:30:03 PST
