[gmx-users] Calculating bond energy

[Erik Marklund]

Bond disociation energies.. Don't you need QM for that? I guess you 
could meassure the difference in bond stretch energy (and angle bending 
and tortions if you like) between the systems and from that estimate the 
change in dissociation energy. Is that what you aim to do?

/Erik

Yulia Einav skrev:
> Thank you for your reply, Mark.
> My protein has four disulfide bonds. I did in silico mutation of one of them and, then, MD simulations. Now I want to know whether breaking one bond influence the others. I can measure the distance between the centers of mass of two sulfur atoms, but is it sufficient to supply the information about bond strength of each disulfide? I guess I mean the bond dissociation energy (not the average one, but rather for each bond individually) of the remaining S-S bonds in the protein.
> Thanks!
>  
> Yulia Einav Ph.D. 
>  
> Mathematical Biology Unit
> Department of Applied Mathematics
> Faculty of Sciences, H.I.T. 
> 52 Golomb Str. POB 305, Holon 58102, Israel.
> Tel. 972-3-5026769, Fax. 972-3-5026769
> E-mail: yulia_e at hit.ac.il, Web: http://www.hit.ac.il <http://www.hit.ac.il/> 
>
> ________________________________
>
> From: gmx-users-bounces at gromacs.org on behalf of Mark Abraham
> Sent: Wed 5/28/2008 14:53
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Calculating bond energy
>
>
>
> Yulia Einav wrote:
>   
>> Dear Gromacs users,
>>
>> After performing MD simulations I want to calculate bond energy for the
>> disulfide bond present in the simulated structure. I didn't find the
>> option for doing this under g_energy command. Does any one know how to
>> do this type of analysis?
>>     
>
> "Calculate bond energy" is too vague... it might been any number of
> things. Can you clarify what you're trying to do, please?
>
> Mark
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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys