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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 03 2021 - 06:00:04 PDT
