Bond between protein and ligand

User discussions
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1

GROMACS version: 2023.4
GROMACS modification: No

Hi,

I have a protein with a non-standard residue which I cut and parametrize with antechamber(acpype). I use pdb2gmx for the rest of the protein to generate top file and use #include for the ligand.itp that was generated.

The problem is that these two are not allowed to bond anymore and [intermolecular_interactions] cant bypass that. What can I do?

Thanks in advance.
Rafail

2

What do you mean with “[intermolecular_interactions] cant bypass that”?

3

Well I thought that I could explicitly state a bond between them but I get “The intermolecular_interaction can not contain chemically bonding interactions”

4

OK. Apparently you need another bond type in [ intermolecular_interactions ]. So, I’m quite sure you can get that working.

But, since this residue is part of a protein I think using [ intermolecular_interactions ] is not the way to go. Try to generate a suitable .rtp entry for your residue instead.

5

I have tried the other bond types (type 6 is allowed because it doesnt explicitly state a bond but still doesnt work).
I found this in the documentation " Interactions that correspond to chemical bonds, that generate exclusions, can only be defined between atoms within a moleculetype`".
And this "When the molecules are covalently bound, e.g. a ligand binding covalently to a protein, they are effectively one molecule and they should be defined in one [ moleculetype ].
So I dont think it can be done this way.
I am trying the rtp method now but its a lot more complex and cant get it to work yet.