[gmx-users] Advice needed

[Priya Das]

Thankyou Justin.

On Tue, Mar 31, 2015 at 5:12 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/31/15 5:25 AM, Priya Das wrote:
>
>> Dear all,
>>
>> I am working with a transmembrane ion channel and have docked a ligand
>> which binds to its pore.
>> The ligand forms only one hydrogen bond with the ion channel.
>> I want to prove the stability of the binding of this ligand using
>> protein-ligand dynamics.
>>
>> 1) Do i need to convey to the system about the hydrogen bonds , i.e.,
>> between which atoms are the hydrogen bonds formed ?
>>
>>
> Hydrogen bonds arise principally due to electrostatic interactions.  You
> don't provide any sort of information about "this is a hydrogen bond" as
> part of any input.
>
>  2) Is gmx hbonds the command for it?
>>
>>
> As the name implies, yes.
>
>  3) In the tutorial (
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>> gmx-tutorials/complex/01_pdb2gmx.html)
>> , there is no mention about forming any hydrogen bonds between ligand and
>> protein , then how do we judge that the protein- ligand affinity is stable
>> in that site or in that conformation?
>>
>>
> Hydrogen bonding is one of many possible stabilizing interactions.  There
> is a whole lot more to the story of protein-ligand binding than just
> hydrogen bonds.
>
> -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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
*Let us all join hands to save our " Mother Earth"*
------------------------------------------------------------------------
Regards,
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala