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
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 23 2015 - 04:00:05 PDT
