VMD-L Mailing List

From: marco di gennaro (marcodigennaro_at_outlook.com)
Date: Tue Mar 16 2021 - 03:06:35 CDT

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 lammps.data
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: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/1355.html 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 lammps.data produced.
Nevertheless there is neither angles nor dihedral angles in the lammps.data 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