> I am trying to do hbond
> using ptraj in amber 9
...
> trajin tmd_jun.mdcrd
> donor mask :1-40.O
> acceptor mask :1-40.N
> acceptor mask:1-40.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.N :1-40.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 hbond.in
ptraj requires an AMBER prmtop or CHARMM PSF to run in order to understand
atom names, etc.
$AMBERHOME/exe/ptraj prmtop < hbond.in >& hbond.out
--tec3
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 20 2009 - 14:04:09 PDT
