Dear Users,
I found, if I use use_sander=1 in the general section, then problem solved.
Can anyone please explain why this ?
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
On Thu, Feb 25, 2016 at 6:24 PM, Indrajit Deb <biky2004indra.gmail.com>
wrote:
> 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 - 16:30:03 PST
