[gmx-users] Creating top-file for molecules not included in the forcefield

Sascha Rehm SaschaRehm at gmx.de
Thu Jan 15 16:14:46 CET 2009

Dear users,

quite some weeks ago I asked you for help in creating some organic 
solvents with the OPLS force field.
I read chapter 5 and started to build the molecule structures and also 
the corresponding itp-files. Since all of the needed atom types were 
found in the OPLS forcefield, this worked fine.

One question I couldn't figure out was how I get the top-file.
I wanted to convert my solvent molecule with pdb2gmx into a .gro file, 
add a box und fill it with more of the solvent molecules, to get a pure 
solvent system.
But pdb2gmx doesn't know the molecule (of course, because it's not a 
residue known to the forcefield). Normally I would add a "#include 
solvent.itp" - line in the topology file of a system, so that gromacs 
can deal with the unknown molecule (like I do when solvating a protein 
with water). But in my case there is no topology-file, so I cannot 
include an .itp-file

Question: Can someone tell me, how I can connect my molecule to my 
.itp-file to build up a pure-solvent-system ? How do I continue after 
building a structure and itp-file?

I couldn't figure it out in the manual and didn't find anything in the 
mailing list :-/

Thanks a lot,

More information about the gromacs.org_gmx-users mailing list