Hai,
I trying to calculate the free energy of binding for DNA+ligand system
using explicit solvent and implicit solvent simulations using amber11 and
ff10. I have successful equilibrated the system for 10ns using implicit and
explicit solvents. When I am calculating the binding enthaplies using PBSA
for implicit solvent system it is giving the following error:
/home/srg/mhb75/Download/amber11/bin/MMPBSA -O -i mmpbsa.in -o final.dat
-sp complex_exp.prmtop -cp com.prmtop -rp rec_imp.prmtop -lp lig_imp.prmtop
-y *.mdcrd &
[1] 23404
geuel% Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
ptraj found! Using /home/srg/mhb75/Download/amber11/bin/ptraj
mmpbsa_py_energy found! Using
/home/srg/mhb75/Download/amber11/bin/mmpbsa_py_energy for PB calculations
Preparing trajectories for simulation...
10 frames were read in and processed by ptraj for use in calculation.
Beginning PB calculations with mmpbsa_py_energy...
calculating complex contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 21.7227
Reaction field energy -6461.1950
Cavity solvation energy 23.6629
PB Bomb in pb_atmlist(): maxnba too short
Error: mmpbsa_py_energy error during PB calculations!
NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
--clean to erase these files.
I have tired to debug the problem by looking into the manual, MMPBSA.py and
related scripts, but couldn't slove the problem. Any idea how to slove the
problem.
The MMPBSA.py script is working fine for the explicit solvent simulations.
Thanks,
mani
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Received on Tue Nov 01 2011 - 12:00:03 PDT
