VMD-L Mailing List

From: Dave Schall (schalljd_at_gmail.com)
Date: Fri Oct 03 2014 - 12:51:22 CDT

 Yep, just now tried it! I dug a little deeper and found you have fixed
this problem in the most recent version of topotools. You apparently set it
up to sort by atom name (very nice for my purposes). After installing the
newest topotool plugin, everything seems sorted out. Thanks.

Now my files are sorted like such:
# 1 C-C-C
# 2 C-C-C1
# 3 C-C-C2
# 4 C-C-H
# 5 C-C1-H
# 6 C-C2-C

very logical and neat.

I'm not running the new vmd beta, but topotools v1.4 seems to work fine
with whatever I am running for VMD

Snipped from Axel's page:

"Version 1.4The final version of TopoTools-v1.4 scheduled to be released
with VMD version 1.9.2.

This version contains bugfixes and improvements and adds support for
accessing crossterms contributed by Josh Vermaas. This feature requires a
version of VMD newer than 1.9.2a33, but version 1.4 should also work with
older versions of VMD; only the crossterm support will not function
correctly.
New features:
- A new utility function TopoTools::fixupnumtypes which prepends numerical
atom/bond/angle/etc types with leading zeros so they get sorted
consistently and in the correct numerical order with ascii style sorting.
This facilitates maintaining the order of numerical atom/bond/angle/etc
types, e.g. when reading and writing data files from LAMMPS."

On Fri, Oct 3, 2014 at 1:44 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
> 

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