I have copied the parm_setup.py to $AMBERHOME/bin/MMPBSA_mods/
After re-run of MMPBSA.py I encountered following error
ERROR:
Loading and checking parameter files for compatibility...
CHAMBER prmtops found. Forcing use of sander
sander found! Using /home/vj/amber14/bin/sander
cpptraj found! Using /home/vj/amber14/bin/cpptraj
Preparing trajectories for simulation...
9 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning quasi-harmonic calculations with /home/vj/amber14/bin/cpptraj
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
File "/home/vj/amber14/bin/MMPBSA.py", line 96, in <module>
app.run_mmpbsa()
File "/home/vj/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 363, in run
Calculation.run(self, rank, stdout=self.output)
File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
self.prmtop))
CalcError: /home/vj/amber14/bin/cpptraj failed with prmtop
2itp_mmpbsa.prmtop!
Exiting. All files have been retained.
On Fri, Apr 24, 2015 at 12:49 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> Now I remember why the issue sounds familiar. Morgan Lawrenz found this
> issue and fixed it quite some time ago (back in November). You can see her
> post here: http://archive.ambermd.org/201411/0274.html. She contributed
> her fix back and I incorporated it into the developmental version of
> MMPBSA.py. But I don't believe the fix was ever turned into an update.
>
> I've attached the fixed parm_setup.py file that Morgan sent me way back
> when. If you copy it to $AMBERHOME/bin/MMPBSA_mods/ then it should fix
> MMPBSA.py. Then you just have to re-run the MMPBSA.py calculation.
>
> HTH,
> Jason
>
> On Thu, Apr 23, 2015 at 8:06 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > This sounds like an error that I've already fixed, but I can't recall for
> > sure. Can you send me, off-list, a compressed tarball containing the
> > topology files, input file, and a trajectory with 2 frames? (You can use
> > cpptraj to extract 2 frames).
> >
> > I will try to have a look and see if I can reproduce the error.
> >
> > Thanks,
> > Jason
> >
> > On Thu, Apr 23, 2015 at 7:48 AM, vijay kumar narsapuram <
> > nvijay1991.gmail.com> wrote:
> >
> >> No,I didn't apply any update after installation of ambertools14.
> >>
> >>
> >> On Thu, Apr 23, 2015 at 4:32 PM, vijay kumar narsapuram <
> >> nvijay1991.gmail.com> wrote:
> >>
> >> > Version is reported as <version>.<patches applied>
> >> >
> >> > AmberTools version 14.25
> >> >
> >> >
> >> > On Thu, Apr 23, 2015 at 4:29 PM, Jason Swails <jason.swails.gmail.com
> >
> >> > wrote:
> >> >
> >> >> Have you applied all updates to AmberTools 14?
> >> >>
> >> >> What is the output of $AMBERHOME/update_amber --version
> >> >> ?
> >> >>
> >> >> On Thu, Apr 23, 2015 at 6:15 AM, vijay kumar narsapuram <
> >> >> nvijay1991.gmail.com> wrote:
> >> >>
> >> >> > Hello Sir,
> >> >> >
> >> >> > I have tried to calculate quasi-harmonic approximation for my
> >> systems as
> >> >> > suggested.
> >> >> >
> >> >> > Input:
> >> >> > &general
> >> >> >
> >> >> > startframe=1, endframe=1, verbose=2, keep_files=0,
> >> >> > entropy=1,
> >> >> > /
> >> >> > &gb
> >> >> > igb=2, saltcon=0.150,
> >> >> > /
> >> >> >
> >> >> > command:$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -cp
> >> >> 2itp_implicit.prmtop
> >> >> > -y newpdb.pdb
> >> >> >
> >> >> > ERROR:
> >> >> > Loading and checking parameter files for compatibility...
> >> >> > CHAMBER prmtops found. Forcing use of sander
> >> >> > sander found! Using /home/vj/amber14/bin/sander
> >> >> > cpptraj found! Using /home/vj/amber14/bin/cpptraj
> >> >> > Preparing trajectories for simulation...
> >> >> > 1 frames were processed by cpptraj for use in calculation.
> >> >> >
> >> >> > Running calculations on normal system...
> >> >> >
> >> >> > Beginning GB calculations with /home/vj/amber14/bin/sander
> >> >> > calculating complex contribution...
> >> >> >
> >> >> > Beginning quasi-harmonic calculations with
> >> /home/vj/amber14/bin/cpptraj
> >> >> > Error: [matrix] Not all arguments handled: [ ,0-328 ]
> >> >> > 1 errors encountered reading input.
> >> >> > File "/home/vj/amber14/bin/MMPBSA.py", line 96, in <module>
> >> >> > app.run_mmpbsa()
> >> >> > File "/home/vj/amber14/bin/MMPBSA_mods/main.py", line 218, in
> >> >> run_mmpbsa
> >> >> > self.calc_list.run(rank, self.stdout)
> >> >> > File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 79,
> in
> >> >> run
> >> >> > calc.run(rank, stdout=stdout, stderr=stderr)
> >> >> > File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 363,
> >> in
> >> >> run
> >> >> > Calculation.run(self, rank, stdout=self.output)
> >> >> > File "/home/vj/amber14/bin/MMPBSA_mods/calculation.py", line 148,
> >> in
> >> >> run
> >> >> > self.prmtop))
> >> >> > CalcError: /home/vj/amber14/bin/cpptraj failed with prmtop
> >> >> > 2itp_implicit.prmtop!
> >> >> > Exiting. All files have been retained.
> >> >> >
> >> >> > let me know if any further details are required if necessary.
> >> >> >
> >> >> > Thank you in advance
> >> >> >
> >> >> > Regards
> >> >> > Vijay
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Sun, Mar 29, 2015 at 3:40 AM, David A Case <
> >> case.biomaps.rutgers.edu
> >> >> >
> >> >> > wrote:
> >> >> >
> >> >> > > On Sat, Mar 28, 2015, vijay kumar narsapuram wrote:
> >> >> > > >
> >> >> > > > I have successfully calculated DeltaG for my systems for namd
> >> >> generated
> >> >> > > > trajectories using CHAMBER in Parmed-Master and MMPBSA.py in
> >> >> > > Ambertools14.
> >> >> > > > For calculating overall free energy change, I need to remove
> >> >> > vibrational
> >> >> > > > entropy part form the DeltaG calculated.
> >> >> > >
> >> >> > > Not sure why one would want to do this....but the normal mode
> >> output
> >> >> > files
> >> >> > > will have the decomposition of the vibrational free energies into
> >> >> > enthalpy
> >> >> > > and entropy terms. So all you should have to do is to extract
> the
> >> >> > > vibrational
> >> >> > > entropy from each output file and average the results.
> >> >> > >
> >> >> > > ....dac
> >> >> > >
> >> >> > >
> >> >> > > _______________________________________________
> >> >> > > AMBER mailing list
> >> >> > > AMBER.ambermd.org
> >> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> > >
> >> >> > _______________________________________________
> >> >> > 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
> >> >>
> >> >
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
>
>
>
> --
> 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 Thu Apr 23 2015 - 13:00:02 PDT
