Hullo,
I am trying to calculate the binding free energy of Tubulin when it
binds with colchicine using mmpbsa.py. I thought of carrying out the
binding energy calculation using both the MM-GBSA method and the
MM-PBSA method for comparison. I am using Amber tools 1.5. In a folder
I have the .top files for the solvated complex,complex in vacuum,
protein in vacuum and the drug in vacuum. Also the .crd files for the
complex , the starting structure generated from leap, the structure
after equilibration, and the structure after 10 ns of simulation.
The input file for mmpbsa:
Input file for running PB and GB in serial
&general
endframe=50, keep_files=2,
/
&gb
igb=1, saltcon=0.100,
/
&pb
istrng=0.100,
/
Then I type in the command to run mmpbsa:
MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
1sa0-water.prmtop -cp 1sa0.prmtop -rp 1sa0_b.top -lp cn2.prmtop -y
*crd
The program stops after giving this error message:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/pinak/amber11/bin/ptraj
mmpbsa_py_energy found! Using /home/pinak/amber11/bin/mmpbsa_py_energy
for GB calculations
mmpbsa_py_energy found! Using /home/pinak/amber11/bin/mmpbsa_py_energy
for PB calculations
Preparing trajectories for simulation...
151 frames were read in and processed by ptraj for use in calculation.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
Error: mmpbsa_py_energy error during GB calculations!
I don't know where is it going wrong. Any help would be appreciated.
Thanks in advance,
--
Devlina Chakravarty
JRF
Bose Institute
Kolkata
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Received on Tue Sep 13 2011 - 06:00:15 PDT
