On 8/20/12 1:46 PM, sai nitin wrote:
Dear all,
Recently i performed 10ns protein ligand simulation and also ran 10ns
simulation only for ligand in solvent obtain parameters for g_lie to
determine DGBind values.
I calculated -Elj -Eqq values from ligand only simulation energy
file... this is where im stuck :(
-Elj = Lennard-Jones interaction between ligand and solvent
-Eqq = Coulomb interaction between ligand and solvent
Im not clear which energy terms should be taken for g_lie caluclation
LJ-SR: LIG-rest or LJ-LR: LIG-rest or LJ-l4:LIG-rest for -Elj ??
Coul-SR:LIG-rest or Coul-l4 : LIG-rest for -Eqq ??
1-4 interactions are intramolecular. These terms should be equal to zero.
Note that if you used PME for any of these calculations, you will have to use
the mdrun -rerun feature with a modified .mdp file. This topic has been
discussed within the last few days on this list.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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