Thank you jason swails for giving valuable inputs.
Previously I was trying with below command:
command: mmpbsa.py -O -i mmpbsa.in -cp complex.prmtop -y complex.dcd
which gave me error as posted to you previously.
After going through Morgan Lawrenz post :
http://archive.ambermd.org/201411/0274.html
I have tried with complex:
Command:mmpbsa.py -O mmpbsa.in -cp complex.prmtop -rp receptor.prmtop -lp
ligand.prmtop -y complex.dcd
This is running successfully without any error; hope I will get some
reasonable values.
Thank you
Regards
Vijay
On Fri, Apr 24, 2015 at 5:29 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 24 2015 - 08:00:02 PDT
