No, I did not get them. Do not try to send the tarball to the amber list.
Please send them to me privately at jason.swails.gmail.com (this is what is
meant by off-list).
On Thu, Apr 23, 2015 at 12:50 PM, vijay kumar narsapuram <
nvijay1991.gmail.com> wrote:
> have you received the compressed tarball..?
> I got a mail(amber-bounce) which states memory issue with that mail.
> please notify me such that I can send you further information if needed.
>
> Thank you
>
> Regards
> Vijay
>
> On Thu, Apr 23, 2015 at 6:02 PM, vijay kumar narsapuram <
> nvijay1991.gmail.com> wrote:
>
> > -PFA
> >
> > let me know if any other files required.
> >
> > Thanks and Regards
> > Vijay
> >
> > On Thu, Apr 23, 2015 at 5:36 PM, 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
> >> _______________________________________________
> >> 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
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Received on Thu Apr 23 2015 - 11:30:02 PDT
