VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Mon Jul 31 2017 - 05:13:44 CDT

I am performing molecule parametrization using ffTK, and almost covered
charge, bond, and angle part. In dihedral part, as the molecule is big with
53 atoms and optimization of the molecule for PES scanning cost much I have
adapted divide and conquer method for dihedral optimization. I wish to
explain the procedure i have adapted for this. I divide the molecule into
three and only my first part is having the penalty. I generated psf /par
and pdb file from mol2 and str generated from cgenff. Now I directly move
to scan torsions tab and generated my input files and get them optimised. I
would like to add a note here that few of the files are scaned for 180 deg
with step size of 6 and few are optimised for 90 degre with same step size.
In the opt torsions tab I get the error as of certain atoms, bonds and
angles are missing. Is there any mistake in the procedure I am carrying out? 

-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*