[gmx-users] Problem with pdb2gmx

[Elham Taghikhani]

Hi

I want to simulate a protein which is bound covalently to a ligand. When I get the gro file of the complex the bond between the amino acid and the ligand is broken although I had modified the .rtp file before and it seems ok in a PDB format.
In the topology, I got this warning message :
Warning:long-bond...
I don't know what should I do to retain the covalent bond.
I will appreciate it if you help me with this problem.