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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 11 Feb 2014 15:05:35 -0800

Okay, I think I've fixed it ... I'm doing tests right now and will
upload in the evening.

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 6:51 AM, Josh Berryman
<the.real.josh.berryman.gmail.com> wrote:
>>>>I think there are still a couple issues.
>
> Yup, like not compiling.  Just a heads up in case noone else has been
> checking the cruise control.  Here's the last bit of the log:
>
> "
> mpif90  -DBINTRAJ -DEMIL -DMPI    -c -O3 -mtune=native -ffree-form
> -I/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/include
> -I/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/include
>    -o pb_force.o pb_force.F90
> pb_force.F90:290.77:
>
>                                    sa_init, sa_driver, sa_free, sa_free_mb,  &
>                                                                            1
> Error: Symbol 'saslave_init' referenced at (1) not found in module
> 'solvent_accessibility'
> make[3]: Leaving directory
> `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/AmberTools/src/pbsa'
> make[2]: Leaving directory
> `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/src/sander'
> make[1]: Leaving directory
> `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/src'
> "
>
> On 11/02/2014, 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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>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
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Received on Tue Feb 11 2014 - 15:30:08 PST
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