AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Thomas Cheatham (
Date: Wed Oct 04 2006 - 17:41:55 CDT

> > donor mask :ADE_at_N1
> > *acceptor mask :THY_at_N3 :THY_at_H3*
> > hbond distance 7 series hbond
> > trajout traj.peptide nobox

p.s. that duplex is fairly big for simulation and contains a lot of
mismatches, G-G, C-C, A-A, T-T; I hope that is what you want... The G-G
and A-A overlaps may be severe enough to lead to stability problems in MD
unless minimized appropriately.

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