Re: [AMBER] CPPTRAJ hbond command

From: Daniel Roe <>
Date: Wed, 29 Aug 2012 10:50:32 -0600


This is my fault. Unfortunately this is the rare case where the manual
was updated and not the release branch of the code. This functionality
does exist and should have been in the release, but as you have
correctly pointed out it is not.

I will look into developing a patch that will put this functionality
into the AT12 version of cpptraj. Right now there is another patch
under development, so I may have to wait until after that is released.
In the meantime, ptraj does have the ability to look at solvent-solute
hydrogen bonds and will print information on bridging waters.

My apologies for the inconvenience.


On Wed, Aug 29, 2012 at 8:35 AM, Samuel Genheden
<> wrote:
> Hello,
> I want to study hydrogen bonds between two proteins and also between
> protein–water–protein, i.e. bridging water molecules between the two
> proteins.
> To my delight I found in the AmberTools12 manual that CPPTRAJ had
> exactly that functionality in the hbond command, with the arguments
> solventdonor, solventacceptor, solvout and bridgeout. However, when I
> run CPPTRAJ with those arguments to hbond they are ignored, and when I
> look in the code, it seems that they are not even implemented.
> Is this so? Do these commands exists in some developmental version
> that I can get my hands on? Or is it possible do the analysis in some
> other way either with CPPTRAJ or PTRAJ?
> Best regards,
> Samuel
> Researcher
> Department och Chemistry and Molecular Biology
> University of Gothenburg
> Sweden
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Aug 29 2012 - 10:00:03 PDT
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