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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>
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Received on Thu Apr 23 2015 - 04:30:03 PDT
