VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Jun 05 2013 - 09:28:19 CDT

Dear Axel

Thank you for your reply,

I explain my problem to you,In my pdb file there aren't any atoms out of
plane by this reason I can not detect

dihedrals for writing in my lammps data file, In your opinion Can I do this
by topo tools? All of my bonds that belong to one molecule are in one
plane,

On Wed, Jun 5, 2013 at 7:03 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Jun 5, 2013 at 2:48 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
> >
> > Dear All users
> >
> > I want to define dihedrals for lammps input data, I could not define by
> > this script :
> >
> > -----------------------
> >
> > .
> > .
> > .
> >
> > topo guessdihedrals
> >
> > vmdcon -info "assigned [topo numdihedraltypes] dihedral types to [topo
> > numdihedrals] dihedrals:"
> >
> > vmdcon -info "dihedraltypes: [topo dihedraltypenames]"
> >
> > ---------------------------------
> >
> > Could any body tell me how I can define these special dihedrals?
>
> the topotools documentation and tutorials demonstrate how they work.
> if it doesn't work for you, you must be doing something wrong, and it
> has to be wrong in the part that you are not showing here. there is
> not much that you can be given.
>
> axel.
>
>
> >
> > --
> > Sincerely
> >
> > Ali Alizadeh
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Sincerely
Ali Alizadeh