[gmx-users] adding a non-residue molecule

[Valentin Gogonea]

Hello gromacs users,

I constructed the topology file (.itp) for a molecule which is not in 
the .rtp file. I run separately pdb2gmx for the protein without cofactor 
and now I want to construct the .tpr file for protein+cofactor. My 
problem is that I have coordinates from a .gro file for protein and from 
a pdb file for cofactor. How can I mix them now? pdb2gmx seems to change 
the coordinates of protein.

I would appreciate any suggestion.

Valentin