Dear all,
I calculated the binding energy using mmgbsa method after fixing the PBC effect in the simulation trajectory. To my surprise, I got the same energy as the result I got without fixing the PBC effect. The following is the job file I used:
solv_parm="tmm2.wet.complex.parm7"
complex_parm="tmm2.complex.parm7"
receptor_parm="tmm2.gas.receptor.parm7"
lig_parm="tmm2.gas.ligand.parm7"
trajectory="11.prod-unwrap.trj"
MMPBSA.py -O -i mmgbsa.in \
-o tmm2_mmgbsa_results2.dat \
-eo tmm2_mmgbsa_perframe2.dat \
-sp ${solv_parm} \
-cp ${complex_parm} \
-rp ${receptor_parm} \
-lp ${lig_parm} \
-y ${trajectory}
The following is the mmgbsa.in file:
&general
interval=1, netcdf=1,
keep_files=0,
/
&gb
igb=8
saltcon=0.0, surften=0.0072,
surfoff=0.0, molsurf=0,
/
&nmode
drms=0.001, maxcyc=10000,
nminterval=250, nmendframe=2000,
nmode_igb=1,
/
I am wondering where was wrong since the protein and ligand are associated in the unwrapped trajectories but they are not in the original trajectories. Thank you very much!
Laura
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Received on Thu Nov 03 2022 - 07:00:02 PDT
