New "names" for ions and carbohydrate?

User discussions
1

GROMACS version: 2021.3
GROMACS modification: No

Dear users,
I’m newbe using GROMACS. So, I want to make sure that I’m not doing something wrong.
I downloaded the new version of the CHARMM files to GROMACS from the MacKerell Lab’s website. When I tried to perform the simulations, the GROMACS showed me an error message about the name of NA and CL atoms. Reading the ions.itp file, it shows that the name of sodium and chloride ions is SOD and CLA.

Following the tutorial from the Lemkul website, I changed the genion “-pname NA -nname CL” command to “-pname SOD -nname CLA”, and created the group SOD_CLA_Water to replace the Water_and_ions in the step that merge protein and ligand (before equilibration steps). So, instead of:

1 (Protein)| 13 (Ligand)
q

I did:

1 (Protein)| 13 (Ligand)
14 (SOD)| 15 (CLA)| 16 (Water)
q

In the MDP file, i changed the

tc-grps = Protein_JZ4 Water_and_ions

for

tc-grps = Protein_LIG SOD_CLA_Water

Is it correct, or did I make a mistake?

Besides, I want to ask if someone could say to me the name of the NAG carbohydrate for the same FF. I couldn’t find it.

Thanks for your help and time.

2

There isn’t one. CHARMM would construct this by adding GlcNAc to the protein residue via its patching mechanism. You would have to introduce a new entry in specbond.dat in GROMACS such that pdb2gmx will create a linkage to the sugar residue (e.g. AGLCNA, BGLCNA, or BGLCN0).

3

Thank you @jalemkul,
Are there any tutorials showing how to perform the preparation of the protein/glycan system?

And the first part of the message, is it ok? Or have I done something wrong?

4

Build it with CHARMM-GUI. Trying to do it in GROMACS is an exercise in frustration.

The ion syntax is fine.