[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jan 27 06:10:46 CET 2010

On 27/01/10 15:58, vivek sharma wrote:
> Hi Dallas,
> I am trying to run MD simulation over a docked complex (protein+ligand),
> to confirm their dynamic stability in water media.
> For the same I am using PRODRG server to generate topologies for ligand
> molecule as gromacs can generate topology for 20 standard residues. As
> mentioned in tutorial for drug-enzyme complex, I am editing the .top and
> .gro files to include the PRODRG generated files (DRGGMX.ITP in .top and
> DRGAPH.GRO in .gro file).
> I observe that their are changes in co-ordinate of ligand after
> processing them through PRODRG server. So these new co-ordinates for
> ligand are placing ligand away from the protein while the ligand
> molecule was in protein pocket in original docked complex.
> I hope it gives what I am trying to do, and where I am getting stuck.
> I am looking for some suggestions and more insight of the problem to
> solve it.
> Earlier I have done same procedure successfully for a different docked
> complex.

So you already have the coordinate file from which you wish to begin MD, 
and all you need are topologies. One approach is to generate your ligand 
.itp file with PRODRG as above, and your protein .top file with pdb2gmx 
from the same coordinate file with the ligand absent. Now you can simply 
take the protein.top file, #include the ligand .itp file and amend the [ 
molecules ] section. This is now a protein+ligand .top file.

Then you will need to take your original protein+ligand structure file 
and perhaps modify the ligand part to conform with the atom and residue 
names and ordering in the PRODRG output coordinate file - but you don't 
need to concern yourself with the coordinates it produces.

As normal, you will need to take care that the coordinate file you 
provide to grompp has the molecules ordered in the same order of the 
[molecules] section, and that atoms within molecules have a 
corresponding ordering in .top and coordinate file.


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