Re: [AMBER] question on mmgbsa energy calculation

From: Bill Miller III via AMBER <amber.ambermd.org>
Date: Thu, 3 Nov 2022 09:04:35 -0500

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 03 2022 - 07:30:02 PDT
Custom Search