AMBER Archive (2006)

Subject: AMBER: H-bond analysis (Ptraj)

From: Esther Brugger (
Date: Thu Nov 30 2006 - 19:28:10 CST

Hello, all,
 I use the Ptraj to do the Hbond analysis, when I run it, it says:
       HBOND output to file output_hbond1.dat,
       data will be sorted, intra-residue interactions will NOT be included,
 I only calculate in the same residue (MIC), I don't know why it doesn't calcuate the Intra-residue interactions.
 Below is my input file. Do you think there is something wrong there? One more questions: what's the meaning of "series" in the H-bond analysis command? Thanks a lot for your help!
 # calculate the H-Bond
 trajin md.mdcrd
 # specify the electron pair DONOR
 donor MIC O15
 # specify the ACCEPTOR(s)
 acceptor MIC N6 H118
 acceptor MIC N7 H129
 acceptor MIC N4 H79
 acceptor MIC N5 H90
 acceptor MIC N2 H40
 acceptor MIC N3 H51
 acceptor MIC N H
 acceptor MIC N1 H11
 donor print
 acceptor print
 hbond out output_hbond1.dat

Esther B.

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