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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Received on Thu Apr 23 2015 - 03:30:02 PDT
