[gmx-users] energy minimization

[rama david]

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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