Hi,
You may also find the cpptraj 'bounds' command useful, which will
determine the min/max Cartesian XYZ values for selected atoms.
-Dan
On Sat, Apr 3, 2021 at 9:12 AM Carlos Simmerling
<carlos.simmerling.gmail.com> wrote:
>
> 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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> >
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Received on Sun Apr 04 2021 - 07:30:02 PDT
