Regarding MMPBSA_BE calculation

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Pooja Singh

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Nov 13, 2023, 5:42:23 AM11/13/23
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These commands I have used sequentially...but command no. 4 is not completed yet after 4 days...how much will it take to complete? 
are all commands OK and their running sequence one after another.?..

mMPBSA analysis commands......

  1. Calculation of potential energy in Vacuum

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -pdie 2 -decomp

2. Calculation of polar solvation energy

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i polar.mdp -nomme -pbsa -decomp

3. Calculation of non-polar solvation energy

(a) For SASA-only model:

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i apolar_sasa.mdp -nomme -pbsa -decomp -apol sasa.xvg -apcon sasa_contrib.dat


(b) For SAV-only model:

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i apolar_sav.mdp -nomme -pbsa -decomp -apol sav.xvg -apcon sav_contrib.dat


4.One step calculation

g_mmpbsa -f md_0_1_noPBC.xtc -s md_0_1.tpr -n index.ndx -i pbsa.mdp -pdie 2 -pbsa -decomp


5. Average Binding Energy Calculation

python MmPbSaStat.py -m energy_MM.xvg -p polar.xvg -a apolar.xvg
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