you could try calculating the radius of gyration, it's a common measure and
can be done in cpptraj.
On Sat, Apr 3, 2021 at 8:43 AM Samanta M <samantamakurat.gmail.com> wrote:
> Dear All,
> I'm trying to find probably very easy thing: the dimension of the protein
> (x,y,z) - in a snapshot (pdb) or even better - in a time series. Let's say
> that the protein is a cube, which should expand on x-dimension during the
> simulation and I need to find the value - how much does it expand (if any)
> comparing to the starting structure. So far I was only able to do the
> simple cpptraj distance between two aminoacids on the edges of the protein,
> but that is not for sure the best way to do it. I do find it expanding, but
> the exact size of the expansion (2-6A) varies from the choice of the
> aminoacids, obviously making it pretty unreliable.
> I would be really grateful for any tips,
> Samanta Romanowska
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Received on Sat Apr 03 2021 - 06:30:03 PDT
