I’m trying to compare the delta-G of binding of a complex using the single- and three-trajectory approach.
In the single trajectory approach, as per manual, th command used was:
mpirun -np 48 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp cmplx_solv.prmtop -cp cmplx.prmtop -rp rec.prmtop -lp lig.prmtop -y *.nc
To get a more accurate estimate of the desolation parts of the energy of the receptor and ligand, I’m trying to use the three trajectory approach. I have run separate trajectories of the complex and one of the subunits.
I looked at the manual but could not find an appropriate flag for the solvated ligand file.
I’d be grateful for any advice on the correct usage.
Regards
George
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Received on Wed Oct 21 2015 - 08:30:05 PDT
