From: John Stone (
Date: Tue Mar 16 2021 - 11:55:50 CDT

  Since GAMESS is quantum chemistry package, I would not normally
expect that its models would include any explicit modeling of the
bonds, angles, dihedrals, etc that a so-called molecular mechanics
based molecular dynamics package like LAMMPS would require.
I expect that you will have to assign appropriate LAMMPS atom types
and define all of those force field terms for the structures you plan
to simulate. Although VMD is able to perform very simple conversions
from one file format to another when they provide/store the same
types of information, it definitely does not automatically assign
atom types or force field parameters, which requires the use of
purpose-built tools that resolve those problems. Hopefully some LAMMPS
users can suggest a good workflow for you to follow to achieve the
modeling you're interested in performing.

Best regards,
  John Stone

On Tue, Mar 16, 2021 at 08:06:35AM +0000, marco di gennaro wrote:
> Dear VMD users,
> I have a GAMESS US output file and would like to export it into LAMMPS
> data format.
> I encounter the following error when using the vmd terminal:
> vmd > topo writelammpsdata
> ERROR) writelammpsdata: need to have non-zero box sizes to write a data
> file
> ERROR) writelammpsdata: current box sizes: {0.000000 0.000000 0.000000}
> I therefore tried to follow
> this: [1] and
> set:
> molinfo top set a 30.0
> molinfo top set b 30.0
> molinfo top set c 30.0
> molinfo top set alpha 90.0
> molinfo top set beta 90.0
> molinfo top set gamma 90.0
> Which kind of made the trick: no error message and produced.
> Nevertheless there is neither angles nor dihedral angles in the
> file.
> Could anyone tell me whether this is the right procedure for GAMESS files,
> and how to improve it/make it properly?
> Thank you
> Best Regards
> Marco Di Gennaro
> References
> Visible links
> 1.

NIH Center for Macromolecular Modeling and Bioinformatics
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University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349