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

From: <leexa.intern.bii.a-star.edu.sg>
Date: Tue, 23 Sep 2014 08:56:55 +0800

Dear Daniel,

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.


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.

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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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> End of AMBER Digest, Vol 985, Issue 1
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Received on Mon Sep 22 2014 - 18:00:02 PDT
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