VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Dec 18 2014 - 12:05:48 CST
On Thu, Dec 18, 2014 at 12:35 PM, Hemant Gangwar
> Hey All,
> I am trying to create lammps data for a protein complex using VMD topotools
> 1.5. I have created psf and pdb file. However when I am trying to save
> lammpsdata file using ;
> "topo writelammpsdata data.protein full", it correctly identifies bond,
> angles and dihedral topology but does not write corresponding coefficients.
> Is there a way to read parameters files (e.g. all_prot.inp etc.) in
> topotools so that it can write all parameters. I am aware of ch2lmp tools
> but I want to work with topotools only if possible as they will not work
> for the extension of this study.
topotools is force field agnostic and thus cannot and will not write
force field coefficients to data files.
the rules how coefficients are assigned to different interactions are
different for each force fields.
if you don't want to use ch2lmp, you will have to write a tool that
parses the topology and atom type assignments and then uses this
information to select the appropriate force field parameters and
finally writes out a file with suitable pair_coeff and bond_coeff and
alike statements that can be used as an include file.
this can be done within VMD or as an external tool.
please note that LAMMPS currently only supports CHARMM force fields up
to about version 22, IIRC. i.e. before the introduction of CMAP
> Please let me know if I need to provide more details. Any help will be
-- 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.