[gmx-users] merger ligand and protein to constriant

Bjoern Windshuegel bjorn.windshugel at uku.fi
Tue Sep 12 14:35:39 CEST 2006


you can also have different chains (Protein and Ligand) and constrain them. 
Using the -merge option you can merge the ligand into the protein but for 
that you need the topology for the ligand (as rtf, not from prodrg). If you 
use Prodrg-topology you first set up the protein without ligand. Then you 
include the topology for the ligand into the protein topology (#include 
XXX.top) and also the coordinates in the protein-gro-file. Then you can 
proceed with adding water, ions, etc. Then you can also apply 

By the way, as far as I know Sonja Schlimme has used a similar kind of setup 
in her MD simulations. So you could also ask her.

Best regards,


> Hi all
>   I already look in the turorial however that is not the thing that I try
> to look for. I would like to merge the ligand into the protein and then
> make the contrain between two atoms, one from the liagand and one from the
> protein. However, as far as I know, I can do the constraint or restraint
> just in the one chain. I cant do that with the different chain. So that i
> try to merge ligand chain and protein chain. I tried to do that with
> pdb2gmx but it is not work. So that i would like to know is there any way
> to merge the ligand chain with the protein chain.
>     Thanks for all your suggstions
> Best Regard
> Kanin

Björn Windshügel

Department of Pharmaceutical Chemistry
University of Kuopio
Harjulantie 1
70211 Kuopio, FINLAND

Phone: (+358) 17 162463
Fax:   (+358) 17 162456

More information about the gromacs.org_gmx-users mailing list