AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Thomas Cheatham (
Date: Tue Oct 03 2006 - 11:05:00 CDT

set prnlev 3 prior to the donor/acceptor specification...

> trajin file.mdcrd
> donor mask
> :47,76,78-84,94,192,193,216,260,264,268,336,361,468_at_NZ,N,NE,NH1,NH2,ND2,OG1
> acceptor mask :1-467_at_O* @H*

also, this is not a 1-1 mapping as there is one O per 2 H; you need 1-1

prnlev 3
acceptor mask WAT O H1
acceptor mask WAT O H2
prnlev 0

...however, this will likely blow memory if you have lot's of solvent...

> hbond distance 3.2 angle 60.0 series hbonds.dat get around that, use the "solventacceptor" command (which keeps
track of waters interacting generally, rather than by specific ID hence is
less memory intensive)

hbond distance 3.2 angle 60.0 series h1 out hbonds.dat \
  solventacceptor WAT O H1 \
  solventacceptor WAT O H2


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