Hello
I’m trying to minimise a protein glycan structure. My protein has multiple chains with one glycated. I had to generate the itp and gro of the glycated chain using tleap and acpype. The other chains I did the normal steps and combined the gro with that of the glycated chain. I added the itp to the topol.top. I added posres but after the energy minimisation, that protein chain and glycan got broken/not connected. Anyone with similar issue using gromacs for simulating protein glycan complex.
Hi @AF1
In classical MD simulations you can’t create/break bonds. If the structure is whole in the topology file (that is, you have bonded terms bonding the glycan and the protein), then formally it is still bound. The absence of a bond is most likely due to the limitation of the visualization software, which usually guesses the topology of the molecules and draws bonds by distance cutoffs.
Thank you. but can the distance increase to like 4 A instead of around 1-2 Angstrom? I measure the distance between the two carbon atom with only three bonds, the fourth being the one that the visualization tool cannot draw and it seems the distance got to around 4 Angstrom. I repeated by applying restraint from the minimisation step itself and it’s still the same.
In principle the length of the bond is defined in the topology, but I would say that 0.4 nm sounds quite long as a bond distance and maybe it’s a problem of the parametrization.
Check the length of the bond in the topology, i.e., check in the bond section what is the equilibrium length. If it’s ~0.4nm then it means that the simulation is behaving as the topology commands, and in that case the problem lies in the parametrization of the molecules.
Thank you. I don’t see anything at 0.4nm in the bonds section. They are all correct reasonable bond length. I’m not sure if the issue is coming from acpype that resulting in missing bonds etc