problems about new molecule parameterization

From: Tian Li (
Date: Thu Jan 30 2014 - 22:28:36 CST

Dear all,

I'm trying to parameterize a new molecule B(OH)3, so far I have used
semi-empirical method to calculated bond length, angle, dihedral angle.
My have two problems:
First, B(OH)3 should be a planar molecule. I modified namd topology file by
adding new atom B, and defined lines. For the IMPR line, I defined only B
 O O O to maintain the planarity of the molecule. Then, I used the new
topology file to generate B(OH)3 psf. file for namd. In the parameter file,
I also modified by putting in all the parameters I have. I'm having trouble
about the Improper and dihedral anlge, because after short time (500 steps)
energy minimization, the B(OH)3 molecule does not stay planar, instead, it
turns to be a tetrahedral geometry. Thus, I'm wondering any one had such
experience? How to maintain the geometry, especially what could be done by
modifying the parameter file or topology file?
My second question is about the Vdw radii of Boron? Any suggestion about
calculating the LJ parameter for Boron?

Thank you in advance,


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