From: Chola Regmi (cholaregmi_at_gmail.com)
Date: Fri Apr 17 2015 - 17:26:03 CDT
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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