From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Oct 03 2014 - 12:44:53 CDT

On Fri, Oct 3, 2014 at 12:08 PM, Dave Schall <schalljd_at_gmail.com> wrote:
> 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
> after.
>
> 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

which version of topotools are you using. have you tried the latest
VMD beta version?

> 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
> files.
>
> Thanks,
>
> Dave
>
>
>
>
> --
> J. David Schall, Assistant Professor
> Dept. of Mechanical Engineering, Oakland University
> 328 Engineering Center, Rochester, MI 48309
> 248-370-2870

-- 
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.