[gmx-users] Development of .ITP or .TOP file for non-standard molecules

[Michelle Hyers]

Hey everyone,

I am trying to setup a MD simulation of non-protein molecules (for
example, C18H37Cl3Si)and I was wondering if there is an easy way to
setup the .top or .itp files for the molecule. I was specifically
wondering if information in the file, such as bonds, pairs, angles,etc.
has to manually determined for each molecule or if there is a way to
output the information from an existing file format such as from a
standard chemical drawing program like ChemDraw or other graphical
interface directly to the require gromacs file types. Any advice about
this issue would be appreciated!

Thanks!

Michelle H.