[gmx-users] Issue with RMSD for protein drug complex

[Sainitin Donakonda]

Hi Justin,

Thank your very much for reply i have done both ways i also have backbone
RMSD data so i will consider only this in my analysis.

Cheers,
Sainitin


On Thu, Jul 4, 2013 at 3:50 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/4/13 5:17 AM, Sainitin Donakonda wrote:
>
>> Hi all,
>>
>> I ran 20ns simulation on protein drug complex..now i want to check overall
>> stability of this complex
>> to acheive this i did following i supplied index file and choose
>> Protein_Lig option for both least square fit and RMSD calculation..i used
>> following command
>>
>> g_rms -f em.tpr (intital structure before production run) -s file.xtc
>> (with
>> out pbc) -n index.ndx -o complex.xvg
>>
>>
>> is this correct way to determine overall stability of the complex ? or
>> should i use only back bone of protein?
>>
>>
> Using the whole complex probably obscures detail.  Using the backbone or
> Calpha atoms is much more common, because it gives you some insight into
> the changes within the fold of the protein.  I guess it all depends on how
> you define "stability" and what you want to measure, but if you're trying
> to assess the stability of the protein's structure, I wouldn't measure it
> like you're doing.
>
> -Justin
>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
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