Protein/cofactor + ligand

User discussions
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1

Dear all,

I mean to do MD simulation of a protein containing a cofactor and a ligand.
I know for ligand I need to have itp to insert in topology file.
But I need to know how I should describe to Gromacs to consider the cofactor as a part of the protein, not as an external molecule.
Do I have to create another itp for cofactor?

I apperciate your responses in advance,
Many thanks,
Best

2

Hi,
as far as I understand, you would like to have one topology describing protein+cofactor, you can try to use pdb2gmx with the option -merge
Best regards
Alessandra

3

Dear alevilla,
Thanks for your response and kindness.

Could you please explain it to me more?
I mean, should I introduce atoms of cofactor to Gromacs force field? or by using -merge can Gromacs distinguish cofactor atoms by itself?
I am working with Gromos53a6.

I apperciate your responses in advance.
Best regards,
MO

4

Hi
What type of molecule is your cofactor? Can you preprocess it with pdb2gmx?
Alessandra

5

Hi,

That is a coenzyme, but I also like to know about both coenzymes and ions.

And, may I have a pdb2gmx command line containing - merge as a template?

Many thanks in advance,
Best

6

Hi,

Coenzymes are usually nonprotein organic molecules. These molecule are not implement in the standard way in the force field, thus it can be not automatically recognized by gmx pdb2gmx.
Thus first you have to get the parameter the coenzyme. You can follow a similar procedure as you did for the ligand (if the ligand was a nonprotein).

Once you have a itp file for the coenzyme. you can include it in topology file. The itp files have to be included in the same order as the molecules appear in the coordinate file.

Ignore the previous suggestions

I hope it helps.
Alessandra

7

To add generally to this discussion:

  1. Nothing in GROMACS cares about whether you call something protein or not, except pdb2gmx, which is only using that nomenclature for checking consistency in a chain.
  2. A non-covalent molecule should generally be parametrized separately and #included later.
  3. A covalent entity should be added as a new residue in the force field and appropriately defined (only case that matters for point 1).
8

In continuation with this, I do have a question… at the time of making index, do we need to make a group of three i.e. protein-coenzyme-ligand?