[AMBER] Obtaining contact maps with cpptraj

From: Stefan Ivanov <bindqgodzgun.abv.bg>
Date: Fri, 23 Nov 2018 06:47:59 +0200 (EET)

 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.
AMBER mailing list
Received on Thu Nov 22 2018 - 21:00:02 PST
Custom Search