AMBER: Using TIP4P water in free energy calculation

From: Lijiang Yang <>
Date: Thu, 5 Aug 2004 15:03:36 -0700

   I have tried to use perturbation topology file to calculate free energy. First, I solvated LEU using TIP4P water and saved a perturbation
topology file. But during my testing, I found that the bonds of LEU residue disappeared in md simulation (by looking at the trajactory in VMD).
What is the reason? Is it a bug? Following is the detailed operations I have done:
 1. load a frcmod file written by myself in xleap, actually this file contains CT and HC information(based on parm99) only, but I
    changed CT to DC, HC to DH
 2.edit LEU, chop off the main chain, change every atoms pertType to DC or DH
 3.solvate it using TIP4P water, buffer=11.0 a perturbation topology file a simulation using options like:
          nstlim=1000, ntpr=1,
          icfe=1, clambda=0.0,
  By the way, I have tested TIP3P, applying the same procedure, bonds are still there.
  Thank you for your response.

Lijiang Yang
Lijiang Yang, Ph.D.
Dr. Ray Luo's Group
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Lab: (949)824-9562
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Received on Thu Aug 05 2004 - 23:53:01 PDT
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