ABF results interpretation

From: HAMID - (h2a1385_at_gmail.com)
Date: Wed Sep 21 2011 - 10:22:38 CDT

Dear NAMD users,

I am seeking any help about the ABF-PMF results interpretation.
I try to enclose the ligand (main group) from bulk water to the
binding site in the receptor lumen (ref group) along Z axis. I use the
distanceZ component and e axis (0,0,-1);

distanceZ {
      main {
         atomnumbers { 1 }
      }
      ref {
         atomnumbers { 2,3,....}
 }
       axis ( 0.0, 0.0, -1.0 )
   }

I followup the ligand movement throughout the trajectory via VMD.
Ligand is in correct path. Then I draw the .pmf file. I confused with
the results. As the ligand be closer to the ligand binding site in the
lumen (lower values of RC) the PMF value be larger (more positive).
Does it mean the ligand has affinity for receptor? I think if the axis
set to (0,0,1) then the positive pmf value means the ligand tends to
move towards larger value of RC along Z-axis. Am I correct?

Best.

----
H. Hadi
PhD student of Biophysics,
UT, Iran

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