Adding SEP and TPO to CHARMM36 ff

GROMACS version:2020.2
GROMACS modification: No

Dear Gromacs Users

I have two phosphorylated residues Serine (SEP) and Tyrosine (TPO) within my pdb model. I am following the step-by-step process on adding a residue to a forcefield as outlined in the following link:

https://manual.gromacs.org/documentation/2020.2/how-to/topology.html

I have updated the residuetypes.dat file within the gromacs installed directory to include the SEP and TPO residues and noted both as Protein. I also copied the charmm36-nov2018.ff folder from the gromacs installed directory and pasted it in my present working directory to edit the merged.rtp file and necessary files. However, I am unsure where to obtain the correct topology defining the atoms, bonds, impropers, etc. for the SEP and TPO residues for CHARMM36 ff.

Can I use CHARMM-GUI or is there a related topology generation tool to obtain these details and adapt the results to the merged.rtp file format?

Thank you, Iris

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CHARMM36 natively support phosphoserine (SP1, SP2), phosphothreonine (THP1, THP2), and phosphotyrosine (TP1, TP2). You don’t need to do anything aside from renaming the residues in your input coordinate file.

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Great, thank you Justin! I appreciate your expedient response. I also reviewed the nomenclature for SP1/2 and THP1/2 atoms and it looks like I will need to change SEP/TPO O3P atom to OT.
Best, Iris

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Hey Justin,

I tried implementing your solution. However, I am still stopped by the error saying THP1211 (211’s the residue number) belongs to the type ‘Other’. The error is the same as before when the name was TPO instead.

Can you please shed some light?
Thanks,
Hemant

Dear Hermant,

if I remember correctly, you should add the affected residue names to the residuetypes.dat file. You will find the “canonical” copy in the “top” directory of your GROMACS installation (e.g. /usr/share/gromacs/top). Make a copy of it and place it to the working directory, and add lines like “THP1 Protein” etc. This way GROMACS tools will recognize these residues as amino acids.

Hope this helps

Kind regards,

Andras

Dear Andras,

Thank you for your response. Your suggestion worked.
Thanks a lot.

Regards,
Hemant