[gmx-users] Protein - Ligand tetramer simulation

Justin Lemkul jalemkul at vt.edu
Thu Aug 9 17:09:07 CEST 2012

On 8/9/12 10:40 AM, Ankita naithani wrote:
> Hi all,
> I am trying to put a tetrameric protein for Energy Minimization to be
> followed by MD simulation of course. But, my problem is that it is a
> tetramer and also I need to perform the simulation with the ligand. I
> have read the tutorial for Protein-Ligand simulation but that explains
> for only one chain, whereas I am talking about 4 chains here.
> I need to put in my tetramer with ligands attached for simulations.
> If I have understood correctly, the tutorial mentions about extracting
> the ligand from PDB and then copying the PDB file of the extracted
> ligand into PRODRG and then retrieving the topology file from there
> and appending it to the topology output of the protein without ligands
> attached. But this is specific for one chain i.e. the PDB co-ordinate
> given to PRODRG is for the ligand from one chain.

Yes, and you would have to acquire properly processed coordinates for each copy 
of the ligand.  You only need one .itp file (which in theory should be the same, 
regardless of which copy of the ligand you input to PRODRG), but you need 
coordinate files for the four copies of the ligands from each chain.  These 
would then be appended to the processed protein coordinate file in the same 
manner as the tutorial suggests.

PRODRG topologies require significant modification to be considered viable for 
real simulation use.  See hints in the tutorial and associated publications.

> The second question is that can I not submit the whole protein-ligand
> complex to GROMACS and then run pdb2gmx for generating topology. How
> do I go about that? I understand that I would have to change the top
> directories of GROMACS to accommodate my ligands but I don't know how
> to do that.

Run pdb2gmx on the protein only, then append ligand coordinates as suggested 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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