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:
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?
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.
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
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.
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.
@bilal
Make sure there is no space between THP1 and the chain so that the residues of the chain match up such as this. Something probably unique about chain start and terminators giving you that error.
ATOM 2878 HD23 LEU A 100 33.178 28.696 15.759 1.00 0.00 PROA
ATOM 2879 C LEU A 100 36.233 33.254 15.058 1.00 0.00 PROA
ATOM 2880 O LEU A 100 37.394 33.567 15.338 1.00 0.00 PROA
ATOM 2881 N THP1A 101 35.282 34.144 14.783 1.00 0.00 PROA
ATOM 2882 HN THP1A 101 34.363 33.863 14.519 1.00 0.00 PROA
...
ATOM 2897 O THP1A 101 35.525 35.316 17.248 1.00 0.00 PROA
ATOM 2898 N GLU A 102 36.885 36.879 16.379 1.00 0.00 PROA
ATOM 2899 HN GLU A 102 37.203 37.389 15.584 1.00 0.00 PROA
PDB files are parsed by number of characters allowed per field and are not space or tab delimited