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

Michelle Hyers mhyers at MIT.EDU
Fri Oct 5 18:42:29 CEST 2007

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!


Michelle H.

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