Hi,
On Mon, Sep 22, 2014 at 6:56 PM, <leexa.intern.bii.a-star.edu.sg> 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.
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.
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.
Hope this helps,
-Dan
>
> SolventAcc TYR_44.HH_751 TYR_44.OH_750
> 19425 2.5900 3.0736 152.8013
>
> Xiong An
>
>> Message: 21
>> Date: Mon, 22 Sep 2014 22:35:38 +0530
>> From: Mary Varughese <maryvj1985.gmail.com>
>> Subject: Re: [AMBER] Hbond Difference For Ambertools 12 and 14, or bug
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>>
>> <CAAjRZU2pvV-yHd3Xa+mW2Hi_iH5k3FFwaqr_3e-f9BAOhb=4LA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>>
>> sir,
>> but what criteria would you prefer than defaults of cpptraj and vmd.?
>>
>> On Mon, Sep 22, 2014 at 7:54 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> On Mon, Sep 22, 2014 at 12:37 AM, <leexa.intern.bii.a-star.edu.sg>
>>> wrote:
>>> > I was comparing my Hbond outputs using the Hbond command from both
>>> > ambertools12, and ambertools14.
>>> > There was discrepency for hydrogen bonding for some types of hydrogen
>>> > bonding between them.
>>> >
>>> > 1. H of water and O of protein was found to be the same
>>> > 2. H of bound to O/N of protein and O of water was found to have very
>>> high
>>> > fractions up to 2.5 compared to an expected maximum of ~1.
>>>
>>> The AmberTools 12 version of cpptraj didn't have the 'solventdonor'
>>> and 'solventacceptor' keywords implemented, so I'm not sure how you
>>> are even comparing them. Without knowing what input you gave to the
>>> AT12 version of cpptraj I can't really answer this.
>>>
>>> > Attached is the relevant files.
>>> > A view of the trajectory in VMD shows hydrogen bonding to only 1 water
>>> > O
>>> by
>>> > the H most of the time, not 2.5 .
>>>
>>> The 'solventacceptor' and 'solventdonor' keywords track *any*
>>> solvent-solute hydrogen bond, which is why the fraction can be greater
>>> than 1. You don't say what criteria you're using in VMD, but note that
>>> the default values in VMD are more strict than the criteria you gave
>>> cpptraj, which may be why you see more hydrogen bonding in the latter.
>>> In VMD the defaults are distance 3.0 Ang., angle 20 (in VMD the angle
>>> is the deviation from 180). However, in your cpptraj run you specified
>>> distance 3.5, angle 120 (which is equivalent to angle 60 in VMD
>>> terms). What happens if you give distance 3.0, angle 160 to cpptraj?
>>>
>>> -Dan
>>>
>>> >
>>> >
>>> > Lee Xiong An
>>> >
>>> >
>>> >
>>> >
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe, PhD
>>> Department of Medicinal Chemistry
>>> University of Utah
>>> 30 South 2000 East, Room 307
>>> Salt Lake City, UT 84112-5820
>>> http://home.chpc.utah.edu/~cheatham/
>>> (801) 587-9652
>>> (801) 585-6208 (Fax)
>>>
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
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>
>
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 22 2014 - 20:00:02 PDT
