AMBER Archive (2006)

Subject: AMBER: ptraj: calculating distances between atoms in charges residues

From: Magne Olufsen (
Date: Fri May 26 2006 - 02:13:48 CDT

I am trying to calculate the distance between the atoms in all charged
residues in AMBER8, and I have read on the reflector site that it should be
possible to calculate distances between heavy atoms in the hbond mode if
the acceptor atoms are specified twise, but it don't work in my case. Do
anyone have any idea why it dosen't work? see my script below.

I will be grateful for any help,

Greetings from Magne Olufsen

#read in the trajectory file
trajin traj1_10.crd 1 999 1
trajin traj11_20.crd 1 999 1
trajin traj21_30.crd 1 999 1
trajin traj31_40.crd 1 999 1
trajin traj41_50.crd 1 999 1
# specify the electron pair DONOR
donor mask :ASP_at_OD1
donor mask :ASP_at_OD2
donor mask :GLU_at_OE1
donor mask :GLU_at_OE2
#-- Acceptors from standard amino acids
acceptor mask :ARG_at_NH1 :ARG_at_NH1
acceptor mask :ARG_at_NH2 :ARG_at_NH2
acceptor mask :ARG_at_NE :ARG_at_NE
acceptor mask :LYS_at_NZ :LYS_at_NZ
hbond distance 6.0 angle 0.0 out ion-contact.txt

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to