On Tue, Apr 30, 2013 at 9:05 AM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Thanks for your answer, Jason. Indeed, I observe "... so use_sav is
> reset to 0." in the mdout files with use_sander=1 (why isn't that
> printed when using mmpbsa_py_energy? isn't that calling the same PBSA
> routines?). So use_sav most probably is not the source of the discrepancy.
>
I think what's happening here is that, while the C code in NAB redirects
stdout to a file unit, the "write(6" statements in the PBSA source code
continues to dump to stdout instead of 'nabout'.
As a result, stdout becomes quite messy, so MMPBSA.py captures and
suppresses that output, for lack of a better idea about what to do.
> So, while we are waiting for someone to comment on this who is more
> familiar with PBSA, I can add that the observations made in
> http://archive.ambermd.org/201304/0131.html could be of the same origin.
>
It's possible, but the OP in that thread uses APBS to do the PB
calculations, so they're more likely unrelated... Do you get similar
answers with sander vs. nab?
Thanks!
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 30 2013 - 07:00:03 PDT
