On Tue, May 24, 2011 at 9:52 AM, Marc van der Kamp <marcvanderkamp.gmail.com
> wrote:
> Many thanks, Jason!
> I now ran the AT15_Amber11.py script before building Amber11 and could
> compile without problems.
> I should have noted that myself...
> Sorry things weren't idiot-proof enough yet for this idiot!
>
Eh, the process is a bit clunky, I'll admit, but it was an easy way to fix
the AT-1.5 + Amber11 building issues without making sweeping changes to the
AT1.5 build process shortly before release (and still maintaining some
semblance of simplicity for users to compile both packages).
>
> Tests run using 'make test' mostly ran ok. There were problems with Steered
> and 'Pinned' MD tests, and I got messages like the following for
> sander_pbsa_frc:
> dbf_2.polyAT
> Cannot match namelist object name cutres
> namelist read: missplaced = sign
> Cannot match namelist object name 5,
>
> checking polyAT force
> FAILED: polyAT force
>
> In addition, there were also 'possible failures' for sander_pbsa_decres,
> sander_pbsa_decpw as well as 02_MMPBSA_Stability, 03_MMPBSA_Binding.
> The mdout.pbsa_decres.dif and mdout.pbsa_decpw.dif files showed only
> marginal changes in the values (typically in the 3rd decimal
> only). Differences in the MMPBSA test_statistics.out.dif files were
> somewhat
> bigger (1st / 2nd decimal), but still not significant it seems. So I
> presume
> I don't really have to worry about this.
>
These are to be expected. PBSA has been changed, so the numerical results
are slightly different (manifesting in changes for all PBSA-enabled tests).
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 24 2011 - 09:00:03 PDT
