HEME-Histidine missing dihedrals

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1

Hello,
I am attempting to simulate a simple heme protein and I am running into an error when I generate ions. I spent lots of time editing my pdb so the heme atom names aligned with the names in the Charmm36 forcefield. I was able to achieve this and I was able to successfully solvate my system. I viewed it in pymol and the coordinating histidine was properly bonded to the iron in the topology and everything looked alright. The topology contains the protein and the heme in the same chain.

Then I moved on to add ions into the system. This is where I am getting errors. It seems as though Charmm36 does not have parameters for Histidine-Heme dihedrals. When I call grompp it gives me these errors:

ERROR 1 [file topol.top, line 32166]:
No default Proper Dih. types

ERROR 2 [file topol.top, line 32168]:
No default Proper Dih. types

ERROR 3 [file topol.top, line 32170]:
No default Proper Dih. types

ERROR 4 [file topol.top, line 32171]:
No default Proper Dih. types

When I look at those lines it is clear that the dihedrals of Fe and various coordinating histidine atoms can not be found. I just started learning molecular dynamics yesterday and practiced with a simple lysozyme system so I do not know what to do now. Am I wrong that Charmm36 does not have the Fe-HIS dihedrals? I used this website: MacKerell Lab

If Charmm36 does have these parameters how do I add them to my system? And if Charmm36 does not have these parameters how can I proceed? Thank you very much!

Thank you,
Elliot

2

The fifth tutorial involves getting parameters for a ligand for the Charmm forcefield, (Protein-Ligand Complex) follow the same procedure and it should work for your system

3

This is a situation in which GROMACS and CHARMM (the program) have a fundamental difference that is very important. There should be no dihedral terms involving the Fe atom. CHARMM allows this case by not automatically generating these dihedrals (the user has control of this via the scripting interface). GROMACS has no equivalent control mechanism and pdb2gmx generates all possible dihedrals. In this case, it is safe to remove any dihedral from the topology that includes the Fe atom.

4

Wouldn’t it then be better to add dihedral parameters that all zero to the force field file for this case?

5

I got the same error , can you briefly ellabrote the steps to solve this issue of HEME protein No default Proper Dih. types ?

6

Hi,

I had to rename the atom names of the HEME to match the names included in the forcefield files. I believe this solved the problem.