AMBER Archive (2006)

Subject: Re: AMBER: hbond analysis

From: Vlad Cojocaru (
Date: Tue Oct 03 2006 - 11:18:28 CDT

Hi Tom,

Thanks for answering but the "acceptor" has nothing to do with waters.
The mask :1-467_at_O* means all possible oxygens in the protein itself.

So, what I am trying to do is set a list of donors (protein atoms) and
find out all hydrogen bonds that these donors make during a trajectory.
That's why I specified all possible acceptors.
For instance I have a ARG ... It makes H.B. with a GLU for the first 100
frames but then it makes another H.B. with an ASP for the next 200
frames. And like this ARG I have other donors that change their
H-bonding partners.

So, I would like to identify all acceptors that make a hydrogen bond
with my donors in at least 1 frame of my trajectory and then to print
out all the info about those hydrogen bonds (distance, angle, occupancy

Best wishes

Thomas Cheatham wrote:

>set prnlev 3 prior to the donor/acceptor specification...
>>trajin file.mdcrd
>>donor mask
>>acceptor mask :1-467_at_O* @H*
>also, this is not a 1-1 mapping as there is one O per 2 H; you need 1-1
>prnlev 3
>acceptor mask WAT O H1
>acceptor mask WAT O H2
>prnlev 0
>...however, this will likely blow memory if you have lot's of solvent...
>>hbond distance 3.2 angle 60.0 series hbonds.dat
> get around that, use the "solventacceptor" command (which keeps
>track of waters interacting generally, rather than by specific ID hence is
>less memory intensive)
>hbond distance 3.2 angle 60.0 series h1 out hbonds.dat \
> solventacceptor WAT O H1 \
> solventacceptor WAT O H2
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Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298

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