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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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