[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position

neeru sharma neeru.bioinfo at gmail.com
Thu Jun 19 11:03:09 CEST 2014

Dear gromacs Users,

I am running a simulation of Protein-Ligand complex. In this case, the
ligand consists of a GTP molecule, whose parameters I am deriving from
PRODRG server.
When I try to generate the complex using coordinates obtained from PRODRG
for GTP and from pdb2gmx for Protein, the position of ligand is not the

I am following these steps in building this protein-ligand complex.

I have followed the same set-up previously, for the same system and it
worked fine then but now it is not.

Can anyone help me out and let me know where I am wrong. Any suggestion
would be welcome.


--Neeru Sharma,
Centre for Development of Advanced Computing (CDAC), Pune, India.

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