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
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Thu Apr 23 2015 - 05:00:03 PDT
