Thanks for clearing that up.
Can you quickly check if all three trajectories have the same total number
of frames?
That is one possible explanation for the length error.
Best Regards
Elvis
On Mon, 14 Jul 2025 at 13:49, Ven, Wouter van de <
w.p.c.v.d.ven.student.tue.nl> wrote:
> Thank you for the response but I feel like I need to clarify a bit better.
>
> I have created the stripped topology and trajectory files and am providing
> them to MMPBSA.py with the flags you suggested. However, it still runs into
> a fatal error at a certain point (AttributeError: 'MultiTrajBinding' object
> has no attribute 'delta2'.) which seems to be originates from a length
> error.
>
> When I look into the temporary files created it becomes apparent that
> there are multiple temporary .inpcrd files created for the complex but not
> for the receptor or ligand. This seems to cause this length error.
>
>
>
> This is why I was looking into the code, hoping to get clarity how the
> length error arises, but there I found this traj.Outtraj which seems off
> since I would expect it to be rectraj.Outtraj in the case of the receptor.
>
>
>
> Hopefully this more clearly explains what I mean and where my confusion
> stems from
>
>
>
> Sincerely yours,
>
> Wouter
>
>
>
>
>
> *From:* Elvis Martis <elvis.afmartis.gmail.com>
> *Sent:* 14 July 2025 12:30
> *To:* Ven, Wouter van de <w.p.c.v.d.ven.student.tue.nl>; AMBER Mailing
> List <amber.ambermd.org>
> *Subject:* Re: [AMBER] MMPBSA
>
>
>
> U ontvangt niet vaak e-mail van elvis.afmartis.gmail.com. Ontdek waarom
> dit belangrijk is <https://aka.ms/LearnAboutSenderIdentification>
>
> 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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>
>
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Received on Mon Jul 14 2025 - 05:30:02 PDT
