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
On Sat, Apr 2, 2022 at 8:56 PM David Poole <thepoole.ucdavis.edu> wrote:
> Hello Jason,
>
> I realized that I could also put this problem up on the github for pytraj,
> https://github.com/Amber-MD/pytraj/issues/1605 , but I will also put the
> two examples here since this is closer to pysander people (perhaps):
>
> We can construct an options set for PB using gas_input as a starting point;
> then use an example trajectory to execute pbsa:
>
> > options = sander.gas_input(8)
> > options.igb = 0
> > options.ipb = 2
>
> fn, tn = get_fn('ala3')
> > traj = pt.Trajectory(fn, tn)
>
> first=pt.esander(traj=traj, mm_options=options)
> > second=pt.esander(traj=traj, mm_options=options)
>
>
> Alternatively, you can just specify igb=10; which also works:
>
> > fn, tn = get_fn('ala3')
> > traj = pt.Trajectory(fn, tn)
> > first=pt.esander(traj=traj, igb=10)
> > second=pt.esander(traj=traj, igb=10)
>
>
> These are both setup to use pytraj/pysander.
>
> Hope this shines some light on it,
> ~David
>
> Hi David,
>
>
> > I don't think I've ever tried the PB interface through the sander API.
> Do
> > you have an example script that shows the error you're seeing?
>
>
> > Thanks,
> > Jason
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Received on Sat Apr 02 2022 - 19:30:02 PDT
