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
> _______________________________________________
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> 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
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Received on Mon Feb 18 2013 - 05:00:03 PST
