[gmx-users] energy minimization

[Onur TUNA]

Dear md,

I think I understand what you want to say. If you want the energy needed to pull away from the binding site, try using Umbrella Sampling method. You will get Potential of Mean Force which you are able to calculate binding constant directly.

Best
Onur

On 11/14/14 08:52 AM, rama david  <ramadavidgroup at gmail.com> wrote:
> 
> Dear md,
>  On docking the only change in enegy for ligand takes place. The protein is
> rigid generally.
> So what was your condition was it regid or flexible for some residues??
> so how it can have the energy the energy of single peptide,single
> protein and the energy of
> docking complex is compared. The docking complex is not always has so much
> less energy.
> which software u used? read the manual of software that may tell about
> there way to compare the enrgy
> and algorithm. what is your aim. what u want to say by analysis??
>  Please mention all these then only someone can suggest you any opinion.
> 
> With regards,
> Rama david
> 
> 
> 
> 
> On Fri, Nov 14, 2014 at 12:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> >
> >
> > On 11/13/14 2:14 AM, md kashif wrote:
> >
> >> Dear all
> >> Can anyone suggest that how to compare change in energy of my protein
> >> before docking and after docking by a ligand.
> >> Please suggest any suitable tutorial or paper if possible.
> >>
> >>
> > You can easily calculate an energy value for the protein (single point
> > energy calculation), but it's not a free energy and it's totally force
> > field-dependent. Proteins are generally (mostly) rigid during docking, so
> > any change in the energy is probably small.
> >
> > If this is related to your previous posts about the energy value after
> > minimization, it's really not a useful quantity because the systems are
> > simply different.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> >
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The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission.


Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez.


The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission.