From: Dave Schall (
Date: Fri Oct 03 2014 - 11:08:27 CDT

Hi vmd-users,

I am converting pdb files to a lammps coord files using vmd/topotools. I
have a system with two types of molecules, say A and B. I am using packmol
to generate pdb files for systems with different mole fractions of A and B.
Packmol generates lists all the A molecules first then, all the B molecules

I take this pdb file and read into vmd, do some atom selections to set
charges/types/masses, etc. I have topotools guess the angles and
dihedrals. Then I dump to a lammps coord file via topotools. I have a tcl
script set up to do this the same way every time.

Since I am running a fairly large set of simulations, I'd like this to be
somewhat automated, but what I find when I inspect the lammps coord files
is that the order of angles and dihedrals is not always the same. This
means I have to check each coord file against my lammps input file to make
sure the order of the parameters match.

For example for some files I get:

# 1 C3-C4-H1
# 2 C-C1-H
# 3 C1-C-H
# 4 C2-C-H
# 5 H1-C3-H1
# 6 C-C2-H

For some others:

# 1 C3-C4-H1
# 2 C-C1-H
# 3 C1-C-H
# 4 C2-C-H
# 5 C-C2-H
# 6 H1-C3-H1

(5 and 6 as switched)

Dihedrals are much more mixed up than angles.

Am I wrong in assuming that if the order of molecules (and atoms therein)
are the same in every pdb file they should be read in the same order by
vmd/topotools? Is this some function of how "topo guessangles" and "topo
guessdihedrals" works? If so I guess I better get busy building a a
parameter database and script that can create input decks from lammps coord



J. David Schall, Assistant Professor
Dept. of Mechanical Engineering, Oakland University
328 Engineering Center, Rochester, MI 48309