Hallo (especially to Dan),
I am trying to become familiar with cpptraj's hbond command. For a
trajectory containing receptor and ligand molecules I am trying to
collect information about all hydrogen bonds formed between receptor and
ligand throughout the trajectory. Hence, my requirements:
- The interest is only in inter-molecular hbonds, not in intra-molecular
ones.
- Both, ligand as well as receptor atoms may serve as donor as well as
acceptor.
- I only need to consider the standard acceptors F, O, N.
From the documentation it is not clear to me how to construct a
corresponding hbond command.
Example: Given two masks of residue IDs, e.g. :1-100 for the receptor
and :101-110 for the ligand, I want hydrogen bonding information printed
to the avgout file (according to the requirements stated above). How
would I do that?
Thanks for your help,
Jan-Philip
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Received on Thu May 02 2013 - 06:00:02 PDT
