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

[Justin Lemkul]

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

-- 
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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 | (410) 706-7441

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