Dear All,
I have simulated a few protein+ligand systems using an explicit solvent
model for 30 ns using ff99SB and amber12. I have calculated the binding
free energies with PBSA and GBSA using mmpbsa.py for all the systems. For
few systems, the binding energy values (both GBSA and PBSA) were in the
order of -800 kcal/mol. In order to get more insights about these values, I
am trying to calculate per-residue decomposition analysis using mmpbsa.py
script of amber12. I am using the following input file for the analysis
GB and PB and decomp
&general
endframe=400, verbose=1,
/
&gb
igb=5, saltcon=0.100,
/
&pb
istrng=0.100,
/
&decomp
idecomp=1, print_res="1-359"
dec_verbose=1,
/
The mmpbsa.py script was successfully executed without the decomposition
analysis inputs. Upon including the corresponding terms for decomposition
analysis, I am getting the following error:
Loading and checking parameter files for compatibility...
Preparing trajectories for simulation...
400 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/amber12/bin/sander
calculating complex contribution...
bad atom type: C0
CalcError: /usr/local/amber12/bin/sander failed with prmtop complex.prmtop!
Exiting. All files have been retained.
sander found! Using /usr/local/amber12/bin/sander
cpptraj found! Using /usr/local/amber12/bin/cpptraj
Did anybody came across this error before? Any help is really appreciated.
Thanks,
mani
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Received on Sat Sep 07 2013 - 16:30:02 PDT
