VMD-L Mailing List

From: winardi, erik (egw24_at_yahoo.com)
Date: Sun Apr 29 2012 - 23:21:01 CDT

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" Am I calling the option wrongly ? 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.