Hi
It is also possible that you can save the complex, receptor and ligand
trajectories in leap while you were preparing the system.
This would be the easiest way.
Other would be use parmed, strip off atoms by each time loading the complex
prmtop, for saving receptor and ligand prmtops.
If you are trying a 3-trajectory approach, that means you have separate
solvated prmtops for each trajectory ( complex, receptor and ligand)
Just strip the waters from the prmtops and trajectories.
Use the following flags in MMPBSA.py -cp, -rp, -lp, -y, -yr and -yl for
complex prmtop, receptor prmtop, ligand parmtop, complex trajectory,
receptor trajectory and ligand trajectory respectively.
I hope this helps.
Best Regards
Elvis
On Mon 14 Jul 2025 at 11:10, Ven, Wouter van de via AMBER <amber.ambermd.org>
wrote:
> Dear all,
>
> I was trying to run a 3-trajectory MM-GBSA calculation on my system but
> kept running into a problem caused by a length error.
> After some thorough debugging, I think I might have found a small mistake
> in the make_trajs.py script.
> Since I’m not entirely sure about this I wanted to post it here so other
> people might confirm/disprove this.
> Line 197 and 243 of the make_trajs.py script contain a traj.Outtraj
> command which I believe should be replaced with rectraj and ligtraj
> respectively.
> When running it after this change it seems to avoid this length error.
> In case my finding is incorrect, I would really like to know why so I can
> continue debugging and understand the code better.
>
> Sincerely yours,
> Wouter
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jul 14 2025 - 04:00:02 PDT
