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
>> >>
>> >
>> >
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 23 2015 - 12:30:02 PDT
