Jason,
works perfect.
Using igb=2, saltcon=0.150,
I've obtained below results for the high affinity agonist of my membrane
receptor (here protein's entropy had not been taken into account):
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -49.2645 3.5945
0.3595
EEL -139.6615 6.8852
0.6885
EGB 136.3443 5.7616
0.5762
ESURF -7.5376 0.1172
0.0117
DELTA G gas -188.9260 7.1462
0.7146
DELTA G solv 128.8067 5.7253
0.5725
DELTA TOTAL -60.1193 3.6655
0.3665
It's looks very good. But why EEL and EGB are so differs in sights?
James
2014-04-26 16:48 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> On Sat, Apr 26, 2014 at 8:35 AM, James Starlight <jmsstarlight.gmail.com
> >wrote:
>
> > Jason,
> >
> >
> > in this log I've found:
> >
> > PB Bomb in pb_aaradi(): No radius assigned for atom 1 N NH3
> >
> > Will it be fixed if my prmtop files for complex receptor and ligand will
> > be created with the assigned radii (e.g using --radii=mbondi2 flag) ?
> >
>
> No -- if you google "PB Bomb in pb_aaradi" it should bring you to some
> threads with suggested solutions.
>
>
> >
> > 2)Also I've found that NM calculations are not possible with the CHAMBER
> > generated prmtops using options from the tutorial. Are the any other
> > possibilities to calculate vibrational entropy terms for such cases ?
> >
>
> You can look at using the quasi-harmonic approximation to approximate
> vibrational modes. It requires a long simulation to converge, though.
> (Alternatively, you can minimize a handful of structures and run very low
> temperature MD (~20-50K) to get results that are almost indistinguishable
> from normal mode analysis, but this is rather uncommon and would need to be
> done by hand since MMPBSA.py doesn't automate this procedure).
>
>
> > 3)Finally what should I provide to the input to use all available CPU
> > cores of my workstation ? (with the default settings only 1 core from 4
> > available on my i5 CPU have been used).
> >
>
> The tutorial has a section about running in parallel -- it's similar to
> running sander or pmemd in parallel (i.e., it is an MPI-parallelized
> program). See
> http://ambermd.org/tutorials/advanced/tutorial3/py_script/section4.htm
>
> HTH,
> Jason
>
>
> >
> > James
> >
> >
> > 2014-04-26 16:26 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >
> >> On Sat, Apr 26, 2014 at 8:12 AM, James Starlight <
> jmsstarlight.gmail.com
> >> >wrote:
> >>
> >> > Jason,
> >> >
> >> > one question. According to below log my GB calculations have been
> >> > successfully finished but PB (with the same input files) result in the
> >> > error during complex processing
> >> >
> >> >
> >> > Beginning GB calculations with
> >> > /home/own/Documents/simulations/amber/amber14/bin/sander
> >> > calculating complex contribution...
> >> > calculating receptor contribution...
> >> > calculating ligand contribution...
> >> >
> >> >
> >> > Beginning PB calculations with
> >> > /home/own/Documents/simulations/amber/amber14/bin/sander
> >> > calculating complex contribution...
> >> > File "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA.py",
> >> line
> >> > 96, in <module>
> >> > app.run_mmpbsa()
> >> > File
> >> >
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/main.py",
> >> > line 218, in run_mmpbsa
> >> > self.calc_list.run(rank, self.stdout)
> >> > File
> >> >
> >>
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> >> > line 79, in run
> >> > calc.run(rank, stdout=stdout, stderr=stderr)
> >> > File
> >> >
> >>
> "/home/own/Documents/simulations/amber/amber14/bin/MMPBSA_mods/calculation.py",
> >> > line 416, in run
> >> > self.prmtop) + '\n\t'.join(error_list) + '\n')
> >> > CalcError: /home/own/Documents/simulations/amber/amber14/bin/sander
> >> failed
> >> > with prmtop complex_dry22.prmtop!
> >> >
> >> >
> >> >
> >> > Exiting. All files have been retained.
> >> >
> >> > Why this should be and does it possible (1) look in some log file on
> the
> >> > reason of such error
> >> >
> >>
> >> Look in _MMPBSA_complex_pb.mdout.0
> >>
> >>
> >> > and (2) obtain results from the GB calculations only? (this time
> >> > FINAL_RESULTS file have not been created).
> >> >
> >>
> >> You can run GB and PB calculations in separate calculations.
> >>
> >> HTH,
> >> Jason
> >>
> >> --
> >> Jason M. Swails
> >> BioMaPS,
> >> Rutgers University
> >> Postdoctoral Researcher
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Apr 26 2014 - 07:30:02 PDT
