If this was just an imaging issue, MMPBSA.py uses cpptraj to re-image any simulations with periodic boundary conditions prior to energy calculations. So that might explain the consistency before and after for your situation.
-Bill
> On Nov 3, 2022, at 8:54 AM, laura zhang via AMBER <amber.ambermd.org> wrote:
>
> 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 - 07:30:02 PDT
