AMBER: ptraj: calculating distances between atoms in charges residues

From: Magne Olufsen <>
Date: Fri, 26 May 2006 09:13:48 +0200

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.OD1
donor mask :ASP.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
#-- Acceptors from standard amino acids
acceptor mask :ARG.NH1 :ARG.NH1
acceptor mask :ARG.NH2 :ARG.NH2
acceptor mask :ARG.NE :ARG.NE
acceptor mask :LYS.NZ :LYS.NZ
hbond distance 6.0 angle 0.0 out ion-contact.txt

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Received on Fri May 26 2006 - 21:05:24 PDT
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