VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 22 2017 - 00:41:16 CST

On Wed, Nov 22, 2017 at 12:40 AM, Vaidyanathan Sethuraman <vsethura_at_umn.edu>
wrote:

> Dear VMD Users
>
> I am using Materials Studio to generate the initial structure for a
> cellulose polymer. Then I export the PDB version to VMD and use topotools
> to generate the input structure for LAMMPS. Please note that the PDB output
> DO contain the CONNECT information (bond information).
>
> Q: Can I use topotools in such a way that it utilizes the CONNECT
> information from PDB file while guessing angles and dihedrals rather than
> using heuristics?
>
> When I use
>
> mol new inpfile.pdb autobonds yes waitfor all
> topo guessangles
> topo guessdihedrals
> topo writelammpsdata out.data full
>
> the output still uses heuristics to compute "BONDS" and generates more
> number of bonds than what is there in the CONNECT info. The reason why
> heuristics is giving more bonds is because of the funky structure that some
> atoms will look apparently close. So can I trick topotools in such a way
> that the angle and dihedral topology is guessed from the CONNECT info?
>

​this has nothing to do with topotools. topotools uses the information that
VMD provides, which in turn depends on the PDB reader molfile plugin.
please look up the "mol" command documentation in the VMD user's guide for
how to tell VMD to not guess bonds.
an even better option would be to use a more suitable file format. PDB is a
rather bad choice for many reasons.

axel.​

>
>
> Best Regards
>
> Vaidyanathan M S
>
> Postdoctoral Fellow
> Kevin Dorfman's Group
> Department of Chemical Engineering and Materials Science
> University of Minnesota Twin Cities
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.