Re: Calculation of PMF between protein domains NAMD

From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Fri Apr 17 2015 - 18:22:17 CDT

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.
> When I observed the trajectories I found that not all system of protein
> uniformly moved along z but the weak interaction region of protein moves
> faster than strong keeping COM motion correct with structural deformation.
> For me this gave the information about weak and strong binding sites but not
> the true PMF. I used spring constant 15 kcal/mol/A^2 and pulling velocity
> 1A/ns. Can anyone suggest the best way to calculate PMF between protein
> protein domains using NAMD.
>
> Following is the extra-parameter section I used in NVT ensemble.
>
> #####################################################
> fixedAtoms on
> fixedAtomsFile ref.pdb
> fixedAtomsCol B
> #######################################################
> SMD on
> SMDFile ref.pdb
> SMDk 15
> SMDVel 0.000002 ;#velocity/2fs
> SMDDir 0 0 -1 ;#pulling direction -z
> SMDOutputFreq 50
> ##########################################################
>
> Thank you.
>
> Chola Regmi
> Virginia Tech

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