Hello I would like to report MMPBSApy APBS related bug.
When sander.APBS is used to calculate solvent energy contribution
(sander_apbs=1) wrong
"_MMPBSA_pb.mdin" input file is created by MMPBSApy.
Here is the example:
--------WRONG FORM GENERATED by ACTUAL VERSION OF MMPBSApy----
File generated by MMPBSA.py
&cntrl
nsnb=99999, ntb=0, cut=999.0, imin=5,
igb=6,
/
&apbs
grid='0.5,0.5,0.5', ionc='0.15,0.15',
pdie=1.0, ionq='1.0,-1.0', bcfl=2,
nion=2, calc_type=0, calcforce=0,
sdie=80.0, gamma=0.10493472,
ionrr='2.0,2.0',
/
--------------------------------------------
and the RIGHT desired form
----------------------------------------------
File generated by MMPBSA.py
&cntrl
nsnb=99999, ntb=0, cut=999.0, imin=5,
igb=6,
/
&apbs
grid=0.5,0.5,0.5, ionc=0.15,0.15,
pdie=1.0, ionq=1.0,-1.0, bcfl=2,
nion=2, calc_type=0, calcforce=0,
sdie=80.0, gamma=0.10493472,
ionrr=2.0,2.0,
/
----------------------------------------------
So the problem is with apostrophes in case of parameters:
grid, ionc, ionq, ionrr. These apostrophes should not be there because
sander.APBS then crashes with below listed errors. If the apostrophes are
deleted
and MMPBSApy is started from corrected "_MMPBSA_pb.mdin" file using
parameter
"-use-mdins" then it works perfectly.
Best wishes,
Marek
[mara.node25 G1]$ ./PROVED_ANALYZU_E.sh
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
Bad data for namelist object grid
Bad data for namelist object ionc
Bad data for namelist object ionq
Bad data for namelist object ionrr
MGparm_check: Neither GRID nor GLEN set!
NOsh: MG parameters not set correctly!
Error while parsing input string.
MGparm_check: Neither GRID nor GLEN set!
NOsh: MG parameters not set correctly!
Error while parsing input string.
MGparm_check: Neither GRID nor GLEN set!
NOsh: MG parameters not set correctly!
Error while parsing input string.
File "/opt/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
File "/opt/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
File "/opt/amber14/bin/MMPBSA.py.MPI", line 104, in <module>
app.run_mmpbsa()
File "/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
line
218,
in run_mmpbsa
app.run_mmpbsa()
app.run_mmpbsa()
File "/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
line
218,
in run_mmpbsa
File "/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/main.py",
line
218,
in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
li
ne 82, in run
self.calc_list.run(rank, self.stdout)
File
"/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py",
li
ne 82, in run
self.calc_list.run(rank, self.stdout)
File
"/opt/amber14/lib/python2.6/site-packages/MMPBSA_mods/calculation.py", li
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Sat Mar 26 2016 - 10:30:04 PDT
