hi David Poole,
Please see the pytraj's docs here:
https://github.com/Amber-MD/pytraj/blob/71493e24fa2dbd1adab19cc8828ff43327712830/pytraj/analysis/energy_analysis.py#L32-L37
The take home message is it's safer to explicitly provide a "legit" prmtop
file.
Hai
On Sun, Apr 3, 2022 at 5:16 PM David Poole <thepoole.ucdavis.edu> wrote:
> Hello Hai,
>
> I've initially tried this with a prmtop file for a ligand that I prepared
> with tleap from which I ran into the same problem when I ran it a second
> time. One difference is that I used an in-memory (i.e., pytraj.load()
> instantiated) rather than in-disk trajectory (i.e., pytraj.iterload()
> instantiated) since the in-memory variant gave me some problems (this was
> due to my misusage undoubtedly, but if I find something specific you will
> hear about it :^D).
>
> Hope this helps,
> David
>
> > Oh you need a proper prmtop file for that. So you need to prepare it via
> > Leap
> >
> > traj = pt.iterload(?you.nc?, ?your.prmtop?)
> >
> > Hai
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Received on Tue Apr 05 2022 - 13:00:03 PDT
