>>>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
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>
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Received on Tue Feb 11 2014 - 07:00:03 PST
