[gmx-users] protein ligand complex Energy Minimisation

Patel, Hershna h.patel28 at herts.ac.uk
Fri May 5 13:44:19 CEST 2017

Dear Gromacs users

I am trying to do energy minimisation of a protein-ligand complex. When visualising the output trajectory and .gro file, the structure of the ligand becomes distorted. The same thing happens when constraining all-bonds during EM. After running grompp, there is this note:   ?

In moleculetype 'zinc01509994' 12 atoms are not bound by a potential or
 constraint to any other atom in the same moleculetype. Although
 technically this might not cause issues in a simulation, this often means
 that the user forgot to add a bond/potential/constraint or put multiple
 molecules in the same moleculetype definition by mistake.

?Is this causing problems during EM, if yes then how do I add bonds/potentials/constraints in the same moleculetype?

I am using Gromacs version 2016, and generated the ligand .itp/.top/.gro files using ACPYPE (the ligand conformation was obtained after docking).



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