Fatal error while doing Protein-ligand simulation using GROMACS 2023

[juhi.khurana03]

GROMACS version: 2023
GROMACS modification: Yes/No
Here post your question: Hello Everyone, I am new to GROMACS and was able to run simulation for apo protein while running simulation for protein-ligand complex, I am facing fatal error while assigning terminus type at C terminus. Detailed descriptions of the command along with errors:

Step1: I have separated ligand from protein-ligand complex using the follwong command: grep UNK complex_1.pdb > UNK.pdb

Step2: Deleted the UNK lines from the complex file manually and saved it as a protein.pdb

Step 3: To create the topology file, used the following command: gmx pdb2gmx -f protein.pdb -o protein_processed.gro -ter

Error: Fatal error:
Atom HG in residue SER 2 was not found in rtp entry SER with 11 atoms
while sorting atoms.

So this time I ran the with the following command: gmx pdb2gmx -f protein.pdb -o protein_processed.gro -ignh

Error: Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp

Also not able to attach the protein and ligand files for reference. any suggestions how to share the said files.

Also I have used the charmm36-jul2022.ff file to select the force field.

Thank you in advance.

[FarzaneJP]

Hi, The input structure for pdb2gmx has hydrogen atoms with names that don’t match the force field’s naming convention in the .rtp file. This results in an error because pdb2gmx requires a specific amino acid naming convention.

To resolve this, you can either use the -ignh flag to disregard the hydrogen atoms, allowing pdb2gmx to estimate their positions, or you should rename the hydrogen atoms in the input to match the .rtp file’s convention if you want to keep their positions. This ensures that pdb2gmx functions correctly with the input structure. Seems you have problem with naming of hydrogens and carbon atoms. hope this helps.

[jalemkul]

The solution to the issue with MET patching is described here:

Newest CHARMM36 port for GROMACS

You need to use the -ter option and interactively choose from the prompts as to which termini you want. For polypeptides, you typically want NH3+. The MET1 patch is for carbohydrates, but pdb2gmx thinks it’s the best match because it matches the MET residue name. In this case, it’s the program trying to be too smart (though there are reasons for it that are typically associated with GLY residues).

Use -ter and select a chemically appropriate terminus.

[hpoggemann]

GROMACS Version: 2022.2
GROMACS modification: No
Forcefield version: charmm36-jul2021

Hello,

I try to run pdb2gmx for a protein and also ran into a terminus problem with MET. As recommended I chose the NH3+ terminus but I get the following error:

Fatal error:

Residue 1 named MET of a molecule in the input file was mapped

to an entry in the topology database, but the atom N used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

I already double checked my pdb input, the N is present and has no unusual label. I also checked the charmm aminoacids.rtp and I do not see a difference to the residue in my pdb file.

Any suggestions to fix this problem would be amazing. Thanks in advance.