Re: [AMBER] cpptraj hbond: query on output

From: Daniel Roe <>
Date: Thu, 9 Oct 2014 16:24:35 -0600


On Thu, Oct 9, 2014 at 2:33 PM, George Tzotzos <> wrote:
> I’m trying to work out h-bonds and bridged h-bonds between a ligand and receptor residues ONLY.

If you just want ligand-receptor hbonds You will want to add the
'nointramol' keyword to your 'hbond' command so that intra-molecular
hydrogen bonds are ignored. If you can probably get rid of your
'donormask' and 'acceptormask' keywords and let cpptraj search for
donors and acceptors. What these keywords are doing right now is
looking for hbond donors in your receptor only and hbond acceptors in
your ligand only - you really want both acceptors and donors for each.

> I used the following script
> hbond REC-LIG donormask :1-125 acceptormask :126 out Nhbond.agr avgout REC-LIG.dat bridgeout Bridge.dat solventdonor :WAT solventacceptor :WAT.O
> When I draw (xmgrace) the output Nhbond.agr shows three series REC-LIG[UU], REC-LIG[UV] and REC-LIG[Bridge].
> The output shows the maximum of per frame interactions to be 2 in the case of REC-LIG[UU] series and 12 in the case of REC-LIG[UV]. The difference between the two datasets is not quite clear to me. Any explanation and/or improvement in the above script would be most helpful.

These are described in the Amber 14 manual in the cpptraj hbond
command (28.10.24):

[UU] Number of solute-solute hydrogen bonds.
[UV] Number of solute-solvent hydrogen bonds.
[Bridge] Number of bridging solvent molecules.

Hope this helps,


> I’m attaching a graphical output for easy reference
> Regards
> George
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 09 2014 - 15:30:02 PDT
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