Dear Sir
Here in the command for MMPBSA/MMGBSA calculation following command has
been used
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
ras-raf_solvated.prmtop
-cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd
As per the tutorial instruction the production step was run 4 time for the
analysis for 2ns.
I have query as to whether we will consider the last step for production
prod4.mdcrd for MMPBSA calculation or do we have to consider all the four
steps of production (prod1.mdcrd,prod2.mdcrd,prod3.mdcrd, prod4.mdcrd)
Here for protein-ligand interaction
I used the following command for delta G calcultion by MMPBSA.
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
C1191I_DRG_solvated.prmtop
-cp C1191I_DRG.prmtop -rp C1191I.prmtop -lp DRG.prmtop -y prod4.mdcrd
Regards
Arunima
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Received on Thu Apr 24 2014 - 23:30:02 PDT
