hi Jason,
Thanks for your immediate reply. If that is the case, why the calculation
completed successfully when I considered 20 frames. Can I trust the data
I am getting for 20 frames?
Thanks
Best regards
Aneesh
On Mon, Feb 18, 2013 at 6:01 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Sorry, decomposition with MMPBSA.py is only supported for Amber 11 and
> later.
>
> All the best,
> Jason
>
> On Mon, Feb 18, 2013 at 4:21 AM, aneesh cna <aneeshcna.gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I am trying to do pair-wise energy decomposition using MMPBSA.py script.
> I
> > have Amber 9.0 and Amber 12 tools in my computer. I have copied sander
> from
> > Amber 9.0 to amber12/bin/ folder before doing the MMPBSA calculation.
> When
> > I used first 20 frames from a 2500 frames containing trajectory file, the
> > calculation completed successfully. Below is the input for the same.
> >
> > ########################################################
> > Input file for running PB and GB
> > &general
> > startframe=1, endframe=40, interval=2, verbose=1, keep_files=0,
> > /
> > &gb
> > igb=5, saltcon=0.100,
> > /
> > &decomp
> > idecomp=3, dec_verbose=3,
> >
> >
> print_res="25;64;65;68-70;99;102;103;105;106;109;110;140;143;144;147;158;160;165;167;180;182;183;186;266;267;269;270;273;279;284;288;294",
> > /
> > #########################################################
> >
> > Unfortunately, when I increase the number of frames to 40 the calculation
> > failed with following error message.
> >
> > #########################################################
> > Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > sander found! Using /usr/local/amber12/bin/sander
> > mmpbsa_py_energy found! Using /usr/local/amber12/bin/mmpbsa_py_energy
> > cpptraj found! Using /usr/local/amber12/bin/cpptraj
> > Preparing trajectories for simulation...
> > 40 frames were processed by cpptraj for use in calculation.
> >
> > Beginning GB calculations with /usr/local/amber12/bin/sander
> > calculating complex contribution...
> > calculating receptor contribution...
> > calculating ligand contribution...
> >
> > ValueError: could not convert string to float: *********
> > Exiting. All files have been retained.
> > ########################################################
> >
> >
> > Here is the input for the above calculation.
> >
> > ########################################################
> > Input file for running PB and GB
> > &general
> > startframe=1, endframe=40, interval=1, verbose=1, keep_files=0,
> > /
> > &gb
> > igb=5, saltcon=0.100,
> > /
> > &decomp
> > idecomp=3, dec_verbose=3,
> >
> >
> print_res="25;64;65;68-70;99;102;103;105;106;109;110;140;143;144;147;158;160;165;167;180;182;183;186;266;267;269;270;273;279;284;288;294",
> > /
> > #########################################################
> >
> >
> > can anyone help me to figure out this problem.
> >
> > Thanks in advance
> >
> > Regards
> > Aneesh
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 18 2013 - 21:30:02 PST
