AMBER Archive (2006)

Subject: AMBER: Calculation of Dihedral constants

From: Prashanth Athri (
Date: Thu Oct 05 2006 - 21:36:15 CDT

Dear all,
  I am trying to calculate a dihedral constant for my small molecule, for eventual dynamics simulations with DNA.
  I take my mol2 file and the respective *.frcmod file and use the follwing commands in xleap:
  mods=loadamberparams my_parms.frcmod
  BP=loadmol2 my_mol.mol2
  saveamberparm BP bp.prmtop bp.inpcrd
  After that I use the following file :
  Initial minimization
  imin=1, maxcyc=5000, ncyc=200
  cut=16, ntb=0, igb=1,
  ATOM 1 1
  ATOM 14 16
  Atoms 1, 14 , 15, 16 form the dihedral in question. The constraints are for the same. Since its for a dihedral angle and this has to be fit to quantum calculations, the commands above have to be done from 0 through 90 or 180 at say 10 degree steps. And then this curve fit to the 631G* curve.
  Question1: I am not getting the proper energy values; as in the energy remains constant for angle values of 0 through 80 and then 90 changes by a reasonable amount. Does anyone see any apparent errors in methodology, or do I just need to use more terms of the cos series?
  Question2: Is there any way to monitor and change dihedral values in xleap, I am having to do that using another program, save it and then re-open it using xleap. I know we can use "Twist" to change it but I dont know if we can monitor it (sorry if this is a very rudimentry quest.)
  I would appreacite any advice. Thanks in advance!

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