[gmx-users] Problem in running protein-ligand (Heteroatom type) system: Ligand position not in correct position
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
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.
Centre for Development of Advanced Computing (CDAC), Pune, India.
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