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 - 06:00:02 PST
