Re: Calculation of PMF between protein domains NAMD

From: Chola Regmi (cholaregmi_at_gmail.com)
Date: Fri Apr 17 2015 - 18:50:25 CDT

Thank you all for your valuable suggestions. I would go through the above
mention paper first and will choose proper sampling method as you mention.
Aron your predection is correct it broke around 10 ns as COM distance 10 A.

Chola

On Fri, Apr 17, 2015 at 7:22 PM, Jeff Comer <jeffcomer_at_gmail.com> wrote:

> You'll probably want to read this paper:
>
> http://pubs.acs.org/doi/abs/10.1021/ct400273t
>
> –––––––––––––––––––––––––––––––––––———————
> Jeffrey Comer, PhD
> Assistant Professor
> Institute of Computational Comparative Medicine
> Nanotechnology Innovation Center of Kansas State
> Kansas State University
> Office: P-213 Mosier Hall
> Phone: 785-532-6311
>
>
> On Fri, Apr 17, 2015 at 5:26 PM, Chola Regmi <cholaregmi_at_gmail.com> wrote:
> > Dear all,
> > I used SMD simulation to calculate the PMF between two protein domains. I
> > oriented the domains
> > along the z-axis and applied the force in one domains using backbone
> atoms
> > and kept other domain fixed at its COM of backbone atoms using
> "fixedAtoms
> > on" command. I found the PMF very high as compare to experimental value--90e6ba6e8ad48c2d6d0513f43eee--

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