VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jul 23 2014 - 07:03:17 CDT

On Wed, Jul 23, 2014 at 2:40 AM, Bonakala Satyanarayana
<satyanarayanabonakala_at_gmail.com> wrote:
> 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.

like the name of the subcommand says, it *guesses* impropers. so it
does not even aim to be 100% correct.
if you see there are entries missing, you have to add them manually.
there simply isn't enough information to always find automatically,
what you want. that is why there are commands in topotools to add or
delete topology entries manually.

axel.

>
> Thank you
>
> B.Satyanarayana, Ph. D
> Molecular modeling lab
> JNCASR
> Bangalore 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.