Dear Amber users,
I need by-residue contact maps from an MD trajectory. I know that the nativecontacts command provides this functionality; however, the maps are divided into "native" and "nonnative" with respect to a reference structure or the first frame in the trajectory. I need a map of all contacts, without such a split, which in my case is artificial and meaningless. Is there a way to obtain a map of all contacts, a combination of "native" and "nonnative" contacts, preferably with a timeseries file as well? It occurred to me to increase the cutoff, so all contacts would be "native," but trajectory processing is too slow.
Sincerely,
Stefan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Nov 22 2018 - 21:00:02 PST
