VMD-L Mailing List

From: Bonakala Satyanarayana (satyanarayanabonakala_at_gmail.com)
Date: Wed Jul 23 2014 - 01:40:58 CDT

Dear Sir/Madam,
                         I have a triclinic crystalline system which has
broken molecules at the boundaries of unit cell. These broken molecules are
connected by another side of unit cell. I am using topotools to creat data
file for LAMMPS simulations. I have gotten correct number of bonds, angles
and dihedrals with the help of following commands.
topo retypebonds, topo guessangles(/dihedrals/impropers).

However, in case of impropers, I am not able to get for molecules which are
at the boundaries (broken ones). Please correct me, if I am doing something
wrong. May I request you to get correct script (or procedure) for
impropers. Your help would be greatly appreciated. Thanks in advance.

Thank you

B.Satyanarayana, Ph. D
Molecular modeling lab
JNCASR
Bangalore