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

vivek sharma viveksharma.iitb at gmail.com
Thu Feb 4 14:43:26 CET 2010

Hi Mark,
Thanks for your response, it worked well for few molecule but not for all.
As I mentioned first I am doing docking and then processing receptor through
pdb2gmx and ligand through PRODRG server.
But number of Hydrogen atoms in docked ligand and PRODRG generated topology
are not same. Although, number of Hydrogens are same in PRODRG generated
topology and pdb file but I can't use them as they have modified co-ordinate
than docked ligand, and the docked ligand coordinates can't be used as they
dont have all Hydrogen atom as mentioned in topology file (.itp file).
Can you suggest a way to come out of this problem.

Thanks & Regards,

On 27 January 2010 10:40, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> 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.
> Mark
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