[gmx-users] Protein-Ligand Covalent Bonds

[Jordan Wolfson]

Dear Gromacs Users,

Hello, I am trying to model the folding of a protein with ligands
covalently bound to the protein. However, there is no pdb file for the
system I am trying to run. I have been trying to figure this out for a good
while now and have come to the conclusion that the answer lies in the
[bonds] section of the .top file for the system. I have ran the simulation
with the ligands before, upon using VMD I found that the ligands were just
sitting next to the protein unbound.

In the [bonds] section of the .top file, how can I specify that the ligands
are covalently bound? I have read the gromacs manual a number of times
looking for the answer to no avail. At one point I thought it possible that
the answer might have to do with the function column of the bonds section
but I have not been able to find any literature explaining what that column
means.

Thank you.


Sincerely,

Jordan