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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Received on Mon Feb 18 2013 - 01:30:04 PST
