From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Fri Apr 17 2015 - 17:43:49 CDT
Hi Chola,
The way I like doing this is to use the collective variables module to
do umbrella sampling along some reaction coordinate that describes the
binding process (usually based on coordnum, but unfortunately its broken
in the released binaries of 2.10). Usually this doesn't deform the
protein like an SMD pull would, since the weakest contacts would break
first, and the protein is free to do what it wants, so long as the
coordination number between the two parts is restrained.
-Josh
On 04/17/2015 05:26 PM, Chola Regmi 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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