VMD-L Mailing List

From: Vaidyanathan Sethuraman (vsethura_at_umn.edu)
Date: Tue Nov 21 2017 - 23:40:33 CST

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?

Best Regards

Vaidyanathan M S

Postdoctoral Fellow
Kevin Dorfman's Group
Department of Chemical Engineering and Materials Science
University of Minnesota Twin Cities