[gmx-users] How to include a small organic molecule

[Monoj Mon Kalita]

Dear Gromacs Users

I am new to this mailing list. I am trying to include a small molecule into
lipid bilayer patch which already have another protein molecule. When I
google it then I found a method in the Swissparam website. But, there it is
mentioned how to do that with Charm27 forcefield, and how to generate the
topology file with Charm27 forcefield. But, my idea is to do this with
gromos45a3 forecfield. However I have tried the method with charm27
forcefield, I have edited the atomtype.itp and aminoacids.rtp files in the
root folder. But, when I tried to proceed for SD step with grompp then one
error message is showing which is "Fatal Error: Syntax error - File
Ligand.itp, line 7, Last line read : '[ atomtypes]' Invalid order for
directive atomtypes.

My input file order in the topology file is

;include forcefield paramaeters
#include "chram27/forecefield.itp"
#include "popc.itp"
#include "ligand.itp"

.....
....
....

[molecules]
;compound          #mols

Protein_chain_A      1
POPC                     276
ligand                      1
SOL                       8748


Kindly have a look, and if possible let me know how to proceed with
gromos45a3 forcefield.

-- 


With Regards
Monoj Mon Kalita
Institute of Biophotonics<http://www.ym.edu.tw/biophotonics/eng_version/home.htm>
Fischer's Lab <http://www.ym.edu.tw/%7Ewfischer/group_mon.htm>
National Yang-Ming University<http://nymu-e.web.ym.edu.tw/front/bin/home.phtml>
Taipei, Taiwan
mon.123chem at gmail.com
+886-978014883