AMBER Archive (2004)

Subject: AMBER: Using TIP4P water in free energy calculation

From: Lijiang Yang (lijiangy_at_uci.edu)
Date: Thu Aug 05 2004 - 17:03:36 CDT

Hi ALL,
   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
 4.save a perturbation topology file
 5.run a simulation using options like:
      &cntrl
          nstlim=1000, ntpr=1,
          ntwx=100,
          icfe=1, clambda=0.0,
     /
     &ewald
          vdwmeth=1,
 
  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
e-mail: lijiangy_at_uci.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu