Hi,
It looks like an imaging issue- have you tried looking at it after imaging
it with something like
trajin equil.rst
autoimage
trajout test.pdb
Alternatively, I think VMD can draw the other unit cells with an option
under Graphics/Representations, since your protein tail is likely just
sitting in the box next to the orginal.
Best,
Kenneth
On Tue, Apr 20, 2021 at 1:36 PM Neville Bethel <nevillebethel.gmail.com>
wrote:
> Hi everyone,
>
> I came across an issue I haven't seen before.
> I am trying to solvate and equilibrate a large triangular protein.
> tleap seems to put one of the ends of the protein outside the original
> solvation box (trimer_example_0.png attached).
> This seems fine since there is still plenty of space between this end and
> the next periodic image, but when I try to equilibrate, this edge of the
> protein flies off into space (trimer_example_8.png).
>
> I also attached the output text from the equilibration run. Does anyone
> know what's going on here?
>
> Thanks,
> Neville
>
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Received on Tue Apr 20 2021 - 13:00:02 PDT
