AMBER Archive (2006)

Subject: AMBER: (no subject)

From: Prashanth Athri (athriprashanth_at_yahoo.com)
Date: Thu Oct 05 2006 - 21:34:47 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 min.in file :
  ----------------------------------------------------------
  Initial minimization
  &cntrl
  imin=1, maxcyc=5000, ncyc=200
  cut=16, ntb=0, igb=1,
  /
  Hold
  50.0
  ATOM 1 1
  END
  Hold
  50.0
  ATOM 14 16
  END
  END
   
  ---------------------------------------
  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!
   
  Best,
  Prashanth

                         
---------------------------------
Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu