Here is an example (I have not validated the result yet, just want to make
sure the code runnable)
In [*1*]: *import* *pytraj* *as* *pt*
In [*3*]: traj = pt.iterload("./Tc5b.crd", "Tc5b.prmtop")
In [*4*]: pt.esander(traj, igb=10) # or: pt.esander(traj,
prmtop='Tc5b.prmtop', igb=10)
The data is in here:
https://github.com/Amber-MD/pytraj/tree/master/tests/data
Hai
On Sat, Apr 2, 2022 at 10:24 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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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>>
>
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Received on Sat Apr 02 2022 - 20:00:02 PDT
