[AMBER] Question about using C-F with iRED

From: Darian Yang <darianyang.gmail.com>
Date: Tue, 3 Aug 2021 00:41:56 -0400


I am interested in calculating relaxation rates of C-F vectors for 19F
substituted tryptophan at various indole ring positions from a protein MD
simulation using iRED (implemented in CPPTRAJ).

From my interpretation of the original paper and this previous post in the
mailing list (http://archive.ambermd.org/201403/0250.html), it seems like
to use iRED for C-H is no different than N-H, but the only change would be
to adjust the default N-H bond length (1.02Å) to be more appropriate to C-H

By this same logic, would it be accurate to calculate C-F relaxation rates
using iRED if the NHDist keyword were changed to something more appropriate
for C-F bonds, such as 1.41Å?

Thank you for your help,

Darian Yang
AMBER mailing list
Received on Mon Aug 02 2021 - 22:00:03 PDT
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