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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Received on Thu Apr 23 2015 - 10:00:02 PDT
