Thanks.
Acoot
From: Erik Marklund <er...@xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Sunday, 3 June 2012 7:03 PM
Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
Hi,
Why don't you do the calculations yourself? You have two HB-energy estimators
and Gromacs at your disposal.
I myself have not verified this, but colleagues have seen a good match between
the energy obtained from Espinoza's formula and the populations of HA-distances
in simulations.
Best,
Erik
3 jun 2012 kl. 10.23 skrev Acoot Brett:
Dear All,
>
>I want to know whether the hydrogen bond energy calculated by the hydrogen
>bond energy calculation formula alone is higher than the corresponding energy
>calculated by GROMACS only based on the distance of the key atoms and the
>charge of the key atoms (of course for hydrogen bond no charge are involved).
>
>Cheers,
>
>Acoot
>
>
>From: Erik Marklund <er...@xray.bmc.uu.se>
>To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>Sent: Sunday, 3 June 2012 6:18 PM
>Subject: Re: [gmx-users] Re : How GROMACS calculate the energy of hydrogen bond
>
>On the same topic, Espinoza et al. also developed a good estimator for HB
>energy. See E. Espinosa, E. Molins, C. Lecomte, Chem. Phys. Lett., 285 (1998),
>p. 170.
>
>31 maj 2012 kl. 16.51 skrev ABEL Stephane 175950:
>
>> Hi,
>>
>> Here, my 2 cents worth. You can also estimate (roughly !!) the HB energy
>> between two groups (say NH---CO) by using the Kabsch and Sander function
>> described in Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577−2637).
>>
>> Quoting:" E = qlq2(1/r(0N) + l/r(CH) - l/r(OH) - l/r(CN))*f with q1 = 0.42e
>> and q 2 = 0.20e, e being the unit electron charge and r(AB) the interatomic
>> distance from A to B. In chemical units, r is in angstroms,
>> the dimensional factor f = 332, and E is in kcal/mol. A good H bond has
>> about -3 kcal/mol binding energy. We choose a generous cutoff to allow for
>> bifurcated H bonds and errors in coordinates and assign an H bond
>> between C=O of residue i and N-H of residue j if E is less than the cutoff,
>> i.e., “Hbond(ij)=: [E < -0.5kcal/mole].”
>>
>> To obtain HB energy value E, you need only the distance between the donnor
>> and acceptor groups.
>>
>> HTH
>>
>> Stephane
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 31 May 2012 15:00:05 +0200
>> From: "lloyd riggs" <lloyd.ri...@gmx.ch>
>> Subject: Re: [gmx-users] How GROMACS calculate the energy of hydrogen
>> bond
>> To: Discussion list for GROMACS users <gmx-users@gromacs.org>
>> Message-ID: <20120531130005.302...@gmx.net>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Dear All,
>>
>> I have no clue what specifically you are trying, but I feal bad for all the
>> physicist and quantum chemist whom have provided the software and continued
>> to develop it.
>>
>> Scanning in my free time, it seems a large amount of confusion on what
>> people are trying to do stems from differences in what is taught textbook
>> wise for things.
>>
>> For instance a hydrogen bond to a physicist is an integration over space in
>> 3 dimensions including time and probabilities of occupied spaces (atom
>> position variabilities reflected even more in proteins, ie the necessity of
>> multiple MD runs with different starting conformations), Vs. an organic
>> chemist whom has cut offs, ie angles between two points and set distances
>> between two atoms which generally reflect the means of calculated chemical
>> energies within a range (say 80-90% which represent means, but usually from
>> raw small molecules as determinants), Vs. Biologist whom have tables which
>> either use a set distance and angle and little account of variability over
>> time (ie a hydrogen bond equals 1.4 kCal/mol reflecting the absolute mean),
>> conformations in amino acids, etc...
>>
>> I think with gromacs it is very precise, as even the smallest energies
>> between two interacting atoms is taken into account with accuracy reflected
>> by the force fields used, and how they were derived.
>>
>> Good luck, your going to start seeing more and more a flood of biologist.
>>
>> Stephan Watkins
>>
>> -------- Original-Nachricht --------
>>> Datum: Thu, 31 May 2012 19:54:04 +1000
>>> Von: Mark Abraham <mark.abra...@anu.edu.au>
>>> An: Discussion list for GROMACS users <gmx-users@gromacs.org>
>>> Betreff: Re: [gmx-users] How GROMACS calculate the energy of hydrogen bond
>>
>>> On 31/05/2012 7:46 PM, Acoot Brett wrote:
>>>> Hi Mark,
>>>>
>>>> It is confusing. As you know, for the same hydrogen bond in a protein,
>>>> the related hydrogen bond angle and bond length can vary within a
>>>> scope during the whole simulation process, however this small
>>>> vibration of the hydrogen bond angle and length can lead to
>>>> significant energy change, and correspondingly the energy of a
>>>> hydrogen bond in simulation can be varied significantly. In comparison
>>>> with hydrophobic effect, it would be too much is the energy of the
>>>> hydrogen bond would be not calculated continuously.
>>>
>>> It isn't, if the model physics isn't paramtrized to include it
>>> explicitly - which is the case for all the force fields in GROMACS.
>>>
>>>>
>>>> Could you give some further clarification?
>>>
>>> What are trying to do? Measuring "the strength of a hydrogen bond"
>>> requires you identify a state with and without it and a path between
>>> them over which you can integrate.
>>>
>>> Mark
>>>
>>>>
>>>> Cheers,
>>>>
>>>> Acoot
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Mark Abraham <mark.abra...@anu.edu.au>
>>>> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
>>>> *Sent:* Thursday, 31 May 2012 4:48 PM
>>>> *Subject:* Re: [gmx-users] How GROMACS calculate the energy of
>>>> hydrogen bond
>>>>
>>>> On 31/05/2012 4:42 PM, Acoot Brett wrote:
>>>>> Dear All,
>>>>> The value of the energy of the hydrogen bond has relation with
>>>>> distance and angle of the hydrogen bond related atoms. As for in the
>>>>> simulation process, the distance and angle of the hydrogen bond
>>>>> related atoms may change continuously. Will you please let me know
>>>>> based on which formula GROMACS calculated the value of the energy of
>>>>> the hydrogen bonds?
>>>>
>>>> There is no such formula used in MD force fields implemented in
>>>> GROMACS. The only non-bonded interactions are the ones you already
>>>> know about: electrostatics and VDW.
>>>> Observables like hydrogen bonds and the hydrophobic effect arise from
>>>> them.
>>>>
>>>> Mark
>>>>
>>>> --
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>>>>
>>>
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>
>-----------------------------------------------
>Erik Marklund, PhD
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596, 75124 Uppsala, Sweden
>phone: +46 18 471 6688 fax: +46 18 511 755
>er...@xray.bmc.uu.se
>http://www2.icm.uu.se/molbio/elflab/index.html
>
>--
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
er...@xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html
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