Hi,
The only way I can currently think of to specifically get h-bonds
between only two molecules is with two hbond commands, e.g. (here
receptor mask is :REC and ligand mask is :LIG):
hbond REC-LIG donormask :REC acceptormask :LIG out Nhbond.agr avgout REC-LIG.dat
hbond LIG-REC donormask :LIG acceptormask :REC out Nhbond.agr avgout LIG-REC.dat
You can then construct the total h-bonds observed from Nhbond.agr,
REC-LIG.dat, and LIG-REC.dat.
The issue is that the code currently does not have a simple way to
exclude hydrogen bonds based on what molecule they are in (except for
solvent of course but that's a special case and certainly not
applicable here). I think what the h-bond command needs is a keyword
that will specify tracking of intra-molecular h-bonds only. It's added
to my to-do list.
Hope this helped,
-Dan
On Thu, May 2, 2013 at 6:30 AM, Jan-Philip Gehrcke
<jgehrcke.googlemail.com> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu May 02 2013 - 07:30:02 PDT
