[AMBER] Hydrogen bond analysis

From: <tdo.chem.ucsb.edu>
Date: Thu, 8 Mar 2012 23:48:00 -0800

Hello everyone,

I have a question about hydrogen bond analysis using Ambertools.

I run REMD for a dimer (two identical monomers). I follow the Amber
tutorial for hydrogen bond analysis, here is part of my ptraj script.

trajin traj300K.pdb
#this is a PDB that contains all of the snapshots at 300K obtained from my
REMD simulation.
Acceptor and donor atoms in the side chains of different amino acids.
#-- Backbone donors and acceptors for this particular molecule
# N-H for prolines do not exist so are not in the mask
# System has 22 residues (11 residues per chain, no proline)
donor mask :1-22.O
acceptor mask :2-11,13-22.N :1-22.H
#Terminal residues have different atom names
donor mask .OXT
acceptor mask :1,12.N :1,12.H1
acceptor mask :1,12.N :1,12.H2
acceptor mask :1,12.N :1,12.H3

hbond print .05 series hbt

I run this script using ptraj. There is a segmentation fault (no error in
the output). I then use ccptraj and part of the output is as followed:

  Acceptor DonorH Donor Frames Frac AvgDist
GLY_9.O ILE_18.H ILE_18.N 1313 0.10 2.879
GLY_20.O ILE_7.H ILE_7.N 1129 0.08 2.882
ILE_18.O ILE_8.H ILE_8.N 1054 0.08 2.884
ILE_19.O ILE_7.H ILE_7.N 947 0.07 2.884
ILE_7.O GLY_20.H GLY_20.N 947 0.07 2.880
ILE_7.O ILE_19.H ILE_19.N 932 0.07 2.888

But this is not really what I want. Is there anything I can change in the
script to get
1) the number of hydrogen bonds per frame
2) the hydrogen bond distribution

Thank you very much,


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Received on Fri Mar 09 2012 - 00:00:03 PST
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