VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Apr 29 2012 - 23:52:25 CDT

On Apr 30, 2012, at 12:21 AM, "winardi, erik" <egw24_at_yahoo.com> wrote:

> Dear Dr. Kohlmeyer,
>
> I am sorry for not providing you much information.
> After I saw the example, I could have the data set I want.
> I could write The bond, angle, dihedral type information, but I have problem in guessing the improper angle
>
> This is what I use
> topo guessimproper [tolerance <10>]
>
> and i got error messege of
> invalid command name "tolerance"

And deservedly so.

>
> Am I calling the option wrongly ?

Yes.

Axel

>
> Thanks,
> Erik
> From: Axel Kohlmeyer <akohlmey_at_gmail.com>
> To: "winardi, erik" <egw24_at_yahoo.com>
> Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Sent: Sunday, April 29, 2012 6:18 PM
> Subject: Re: vmd-l: writing pair/bond/angle/dihedral information for lammps input
>
> On Sun, Apr 29, 2012 at 6:17 PM, winardi, erik <egw24_at_yahoo.com> wrote:
> > Hi VMD users,
> >
> > I am having difficulties on writing a script to
> > generate pair/bond/angle/dihedral information for lammps data input
> > (topotools).
> > I attach my sample .car file that I want to write into lammps data input.
> > The system contain two Phenols (with hydrogen being deleted at para and
> > ortho position) and six CH2 molecules.
> > I think the system will have:
> > 5 bond style
> > 5 angle style
> > 4 dihedral style
> > 2 improper style
> >
> > Could anyone help me how to do it ?
>
> documentation and some simple tutorials are here:
> http://sites.google.com/site/akohlmey/software/topotools
>
> if you want help, you have to be *much* more specific,
> since it is not at all clear what exactly you want to
> get done. setting up a simulation topology requires
> much more information than a coordinate file with
> no bonding information at all.
>
> axel.
>
>
> >
> > Thanks,
> >
> > Erik Winardi
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>