Oh right. MMPBSA.py uses some modules from ParmEd to process and
manipulate topology files, and the parm_setup.py file I gave you is not
compatible with the version of ParmEd shipped with AmberTools 14.
AmberTools 15 should be released within the next few weeks, and this bug
should be fixed there. (If you are subscribed to the Amber mailing list,
you will see an announcement when it is released).
All the best,
Jason
On Thu, Apr 23, 2015 at 3:56 PM, vijay kumar narsapuram <
nvijay1991.gmail.com> wrote:
> 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
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Apr 24 2015 - 05:00:03 PDT
