Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug

From: <>
Date: Wed, 24 Sep 2014 10:54:27 +0800

Thanks Daniel and Dac for your help.

I have managed to solve my main problem, and also found some unwanted
problems along the way.

> Hi,
> On Mon, Sep 22, 2014 at 6:56 PM, <> wrote:
>> I have uploaded both ambertools12 and ambertools14 files. The VMD cutoff was
>> done with an angle of 60, and also at 3.5A, which is equivalent to the ones
>> with ambertools.
> First, your AmberTools 12 calculation used ptraj, which has very
> different hydrogen bond functionality. For one thing, the definitions
> of hydrogen bond donor and acceptor are reversed in ptraj compared to
> cpptraj. A brief comparison of the output shows that very different
> numbers of donors and acceptors are defined, so the results shouldn't
> match anyway.

Some problem with my previous definition of acceptors/donors was found.

> Second, in your cpptraj input you specified ':WAT' as your
> solventacceptor mask, meaning all 3 atoms are considered acceptors,
> which is clear from your output:
>> Set up 11172 solvent acceptors
>> Set up 7448 solvent donors
> You probably want to specify only :WAT.O for the solventacceptor mask.
>> One thing that is puzzling is that from basic chemistry,a H only has one
>> hbond, which is why i think that a fraction of 2.5900 for the TYR_44.HH is
>> high, or unless i have made a mistake in the command.

Main problem

Acceptor : Donor ratio is 3:2, not 1:2, which explains why i got a
fraction of 2.5900, as the H was viewing all the H that are near to
its O as a hydrogen bond, ie;H-H is also a hydrogen bond.

> I disagree, particularly for water - just google 'bifurcated hydrogen
> bond'. Remember that in the Amber force field there is by default no
> explicit hydrogen bonding term; those interactions occur within the
> Lennard-Jones/Coulomb parts of the FF equation, so the hydrogen
> hydrogen bonds you get in simulations aren't necessarily hydrogen
> bonds the way a chemist would think of them. A lot may depend on what
> water model you are using as well.
> I think Dave's suggestion of running your calculation on a few frames
> so you can be certain you are setting up your calculation properly is
> an excellent one. In particular pay attention to the output from
> cpptraj about what is being selected. You can specify 'debug actions
> 1' prior to the 'hbond' command to get some more information on your
> solute donors/acceptors.

This debug actions 1 command is very useful!

Xiong An

> Hope this helps,
> -Dan

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Received on Tue Sep 23 2014 - 20:00:03 PDT
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