Subject: substrate exit from protein in Amber 8.0 TI vdw simulation

From: Eric Hu <eric.y.hu !=! gmail.com>
Date: Mon, 21 Mar 2005 10:12:55 -0800

Hi, I am trying to perturb a molecule to nothing in a protein binding
pocket. By looking at the pdb files at the end of each lambda run, the
molecule has migrated out of the protein when clambda is equal to
0.43738 or bigger. One explanation would be that the small molecule
with shrinking vdw radii do not have favorable interactions with
protein any more comparing to water molecules and expelled therefore.
Therefore I wonder if a weak restraint is needed in order to evaluate
the dV/dL ~ L integral. Thanks.

I suspect that this is true for all vdw perturbation calculations.

Eric

&cntrl
  ntr=0,
  nstlim =20000, nscm=2000, ntave=5000,
  ntx=1, irest=0, ntb=1, ntpr=100, tempi=300.0, ig=974651,
  ntp=0, taup=1.0,
  dt=0.001, nrespa=1,
  ntt=1, temp0 = 300., tautp=2.0,
  ntc=2, ntf=2, tol=0.000001,
  ntwr = 100, ntwx=100,
  icfe=1, klambda=6, clambda=0.99078,
 cut=9.0,
/