Dear Users,
I am trying to carryout MMPBSA calculations in serial with AMBER14 and
AMBERTOOLS15 with latest updates. Everything (GB, PB, Quasi harmonic and
Normal mode) is working fine for my control RNA duplex and also for one
mutated duplex. But for another mutated duplex I am getting the following
error....
Running calculations on normal system...
Beginning GB calculations with
/home/indra/amber14-tools15/amber14/bin/mmpbsa_py_energy
calculating complex contribution...
bad value for Pn: 393 396 411 414 7.000
File "/home/indra/amber14-tools15/amber14/bin/MMPBSA.py", line 104, in
<module>
app.run_mmpbsa()
File
"/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File
"/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File
"/home/indra/amber14-tools15/amber14/lib/python2.7/site-packages/MMPBSA_mods/calculation.py",
line 157, in run
self.prmtop))
CalcError: /home/indra/amber14-tools15/amber14/bin/mmpbsa_py_energy failed
with prmtop dry-complex.prmtop!
Exiting. All files have been retained.
If anyone have any idea, please help.
Thanks
----indrajit
--------------------------------------------------------------------------------------------------------------
*Indrajit Deb*
alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
*Present Position*
International Centre for Genetic Engineering and Biotechnology (ICGEB,
Italy) SMART Fellow,
Department of Structural Chemistry and Biology of Nucleic Acids,
Institute of Bioorganic Chemistry (IBCh),
Polish Academy of Sciences (PAS).
European Center for Bioinformatiocs and Genetics (ECBiG) Campus (
R
oom: 2.6.28
).
Z. Noskowskiego Str. 12/14.
Poznan 61-704, Poland.
Phone: +48616653042, Personal Mobile: +48662513522
*Previous Position*
Ph.D Student,
Department of Biophysics, Molecular Biology and Bioinformatics, University
of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
+913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
+919239202278
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Received on Thu Feb 25 2016 - 09:30:04 PST
