VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Wed Jun 05 2013 - 10:22:45 CDT

Dear Axel

Thank you for your reply,

You are right,

I was a bit confused, I wanted to define improper dihedrals,

There isn't any tutorial about it, I do not understand Why should we define
tolerance for detection of impropers?

On Wed, Jun 5, 2013 at 7:07 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Wed, Jun 5, 2013 at 4:28 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> wrote:
> >
> > 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,
>
> i don't understand a single thing you are writing here. what does
> having atoms in a plane do with dihedrals?
>
> what topotools can do is explained in the documentation. you can set
> individual dihedrals any which way you like. you can also use the
> corresponding lowlevel VMD script commands. whether they do what you
> want, depends on whether you use them correctly. there are no checks.
> you ask for it, you get it. garbage in, garbage out.
>
> so it is all up to you.
>
> axel.
>
>
> >
> >
> > 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
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Sincerely
Ali Alizadeh