Can we perform stability analysis for Protein-Ligand?

[Gundala Viswanath]

Hi, 

I'm trying to perform Stability analysis for my protein and ligand, 

Following  that suggestion I have this input file:

&general
sys_name="Stability",
#startframe=5, endframe=21, verbose=2,
startframe=1, endframe=9999999, verbose=2,
protein_forcefield="oldff/leaprc.ff99SB",
/
&gb
igb=2, saltcon=0.150,
/

And the command line I use is this:

mpirun -np 20 gmx_MMPBSA MPI  -O -i  $MMPBAIN   \
    -xvvfile $XVVFILE \
    -cs md.tpr \
    -ci index.ndx  \
    -cg 1 20  \
    -ct md_fit.xtc \
    -lm Ligand.mol2 \
    -nogui \
    -eo FINAL_RESULTS_MMPBSA.stability.csv

Note that in the command line I included -lm Ligand.mol2.

Without that gmx_MMPBSA will break. Is my approach reasonable?

G.V.

[Mario Sergio Valdes]

For stability calculation you must define the -s or  --stability option. Please check this section (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/command-line/#gmx_mmpbsa-command-line) or type gmx_MMPBSA -h for more info