On 9/15/19 7:27 AM, Bratin Kumar Das wrote:
You can see the radius of gyration, number of hydrogen bond, native contact
etc for assessing the stability
Overall, "stability" implies persistence of important interactions
(really it implies knowledge of free energy of the system, but
structural metrics can be reasonable proxies). This may encompass native
contacts (though how one defines "native" may be somewhat difficult to
do), hydrogen bonds, and other interactions. For a globular protein,
radius of gyration is not generally useful.
-Justin
On Sun 15 Sep, 2019, 4:32 PM Quin K, <profiles...@gmail.com> wrote:
Thank you!
What else should I be looking for?
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On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 9/15/19 5:30 AM, Quin K wrote:
Hi everyone!
I have done a MD simulation for a protein structure at 310K (100ns)
this
is
the RMSD at around 65 ns kindly comment on the stability. Will I have
to
rerun the MD?
Kindly let me know how to decide stability by analyzing RMSD.
RMSD alone is generally insufficient to make any definitive conclusions
about stability. I see nothing out of the ordinary in the plot.
-Justin
For backbone
<
https://drive.google.com/file/d/18JjiAKivbWklIXRSVaqhQ2zMUN9L_hkl/view?usp=sharing
For backbone xvg file
<
https://drive.google.com/file/d/12MBTO57f_xROW5mWTFtMskwTNL1gCvam/view?usp=sharing
For protein
<
https://drive.google.com/file/d/1LrdIFxQ-rBrIkcgbnfgEHg424cKgGm7_/view>
For protein - expanded
<
https://drive.google.com/file/d/1yvwLzdYMAenL9n1kOdaVzOo5JU6j4YU-/view>
For protein xvg file
<
https://drive.google.com/file/d/1hKbbTOCLqG7xDySQ7r4VcrNfSaokmYJO/view?usp=sharing
Thank you in advance.
Regards!
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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