[gmx-users] Protein - Ligand tetramer simulation

Ankita naithani ankitanaithani at gmail.com
Thu Aug 9 16:40:31 CEST 2012

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.
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.

I know my question might be really silly but I am short of time at the
moment and would really appreciate any help in this matter.

Best Wishes,

Ankita Naithani

Ankita Naithani

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