From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jun 05 2013 - 09:37:22 CDT

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.