How can I generate a topology for a peptide contain unnatural amino acids and a linker ?

GROMACS version:
GROMACS modification: Yes/No
Here post your question

I am doing an MD simulation of a peptide with 3 unnatural amino acids and a linker using Gromacs. I have already generated the itp files for unnatural amino acids and the linker using ATB web server.

Can anyone suggest to me how to generate topology(.itp and .top) for the whole peptide chain ?

If you have Itp files then you need to insert it to the top and create .gro file from the pdb. This is same as inserting ligand topology from protein-ligand simulation tutorial. On another way you can add the unnatural aminiacoid parameters int he respective files and invoke it hrough gmx pdb2gmx.

Thank you for your suggestion. May I know how can I unnatural amino acid parameters in the forcefield files ?

The only way to incorporate noncanonical residues into a contiguous polypeptide chain is to create .rtp entries for those residues, add them to residuetypes.dat as Protein residues, and add any necessary parameters to ffbonded.itp and ffnonbonded.itp (if necessary). I would contend that this approach has little to nothing to do with my protein-ligand tutorial, aside from potentially using external tools to help parametrize the new residues, but the use of a separate .itp file for nonstandard species is not correct for this task.

1 Like

Thank you @jalemkul . I got the point

Can anyone support me to get the accurate .hbd entry for the "HA’’ hydrogen in the attached molecule?

My following entry gives an error in Gromacs
Screenshot from 2022-01-26 15-57-28

I also want to know the “-C” meaning in .hbd entries

Addition type 5 requires 4 control atoms. See existing amino acids in the .hdb file for how this is done.

The “-” prefix means the atom from the preceding residue in the polypeptide chain. Similarly, “+” means the next residue.

Dear @jalemkul ,

I tried to modify the forcefield (charmm36) for the following unnatural amino acid. I used to charmm GUI , and ligand topology generator to get parameters. May I know, how to get parameters for ffbonded.itp and ffnonbonded.itp for the following residue ?

Combine disulfide and standard alkyl parameters.

can you suggest to me how to combine these parameters?
Is there any tool to do it or manually do it?

It’s not bad to do by hand. The left-hand side of the molecule through the SG atom is just cysteine, and including SD is just the disulfide version of the residue. Everything can come directly from that. The methyl groups on the right-hand side all have fixed parameters, by CHARMM convention, with H atoms bearing 0.09 charge and the bonded C atoms -0.27 to balance them. Then the final CE atom is assigned a charge that renders the species net neutral. The atom typing is also straightforward from model compounds.

There may be some bonded parameters, like an angle or dihedral or two, that aren’t defined, but the parametrization procedure is given in detail in numerous publications.

Dear Justin,

Can you propose how to find the molecule’s angle and dihedral parameters?

By adhering to the force field’s prescribed parametrization methods (optimized geometry, vibrational frequency calculations, potential energy scans).