AMBER Archive (2009)

Subject: RE: [Subject Filtered] [AMBER] hbond-error in amber9 8%

From: Thomas Cheatham III (
Date: Fri May 01 2009 - 13:07:40 CDT

> I am trying to do hbond
> using ptraj in amber 9
> trajin tmd_jun.mdcrd
> donor mask :1-40_at_O
> acceptor mask :1-40_at_N
> acceptor mask:1-40_at_H
> hbond distance 3.2 angle 120.0

The acceptor command is not specified correctly; you need both the
hydrogen acceptor and its heavy atom (i.e. two atoms)

acceptor mask :1-40_at_N :1-40_at_H

Also, likely you would want to add the series keyword.

hbond series h1 out hbond.dat distance 3.2 angle 120.0

> $AMBERHOME/exe/ptraj

ptraj requires an AMBER prmtop or CHARMM PSF to run in order to understand
atom names, etc.

$AMBERHOME/exe/ptraj prmtop < >& hbond.out


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