Re: [AMBER-Developers] one week until code freeze

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 11 Feb 2014 09:45:04 -0800

Okay, I'm looking into this. So far I've only tested sander/pbsa/nab ...
will test mmpbsa.py and mpi version next ...

Ray
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Feb 11, 2014 at 5:32 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, 2014-02-10 at 18:18 -0800, Ray Luo, Ph.D. wrote:
>> The sander/pbsa interface issue has been fixed and pushed ...
>
> I think there are still a couple issues.  The MMPBSA.py tests (which I
> just got working again) are now failing on the sander/PBSA interface.
>
> This is the error I'm getting from the _MMPBSA_complex_pb.mdout output
> file:
>
> File generated by MMPBSA.py
> &cntrl
>  nsnb=99999, ipb=2, ntb=0, cut=999.0,
>  imin=5, idecomp=1, igb=10,
> /
> &pb
>  istrng=150.0, maxitn=1000,
>  fillratio=4.0, radiopt=1,
> /
> Residues considered as REC
> RRES 4 6
> END
> Residues considered as LIG
> LRES 1 3
> END
> Residues to print
> RES 1 6
> END
> END
>
> --------------------------------------------------------------------------------
>    1.  RESOURCE   USE:
> --------------------------------------------------------------------------------
>
> | Flags:
> PB Bomb in pb_read(): ipb can only be larger than or equal to 1.
>
>
> So it seems that somewhere the value if ipb (which is set to 2 in the
> input file) is not being propagated to the PB part?  I can't find an
> obvious place where this is happening and this input file has not
> changed since the AmberTools 13 release (when it worked with Amber 12).
> You can run the 07_Comprehensive test in AmberTools/test/mmpbsa_py for a
> reproducible case.
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Feb 11 2014 - 10:00:07 PST
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