Dear all,
I have two modified nucleotides, pseudouridine and m6adenine, in my RNA molecule. I try different ways, charmm-gui PDB Reader & Manipulator using the whole RNA, to obtain .psf, than Parmed to convert psf in top. I include the charmm36 in the local directory and in the topol.top file.
→ Results: a list of missing values in the topol.top
I try also, CgenFF and cgenff_charmm2gmx.py conversion, but so I obtain a ligand, and I need to include the modified nucleotides in the same chain.
In the case that you need to include residues that don’t exist in the forcefield’s database, you need to include the residue’s topology in the topol.top file yourself. This means you can’t just generate the topol.top file from pdb2gmx, you’ll need to take the topology information from the .itp file and include it in a topol.top file you create manually.
In case you haven’t come across it yet, a good example to follow is this tutorial on creating a topology for a ligand in complex with a protein (Protein-Ligand Complex). Assuming that you’ve already generated the ligand topology data with CgenFF and that the .gro file you’re using already has all the coordinates, you can just skip to adding the #include under “Build the Topology”
I try to use CgenFF (etc), I obtained the *itp, that I use to add my modified nucleotide in cgenff.rtp, add also H in cgenff.hbd and add PSU to residuetypes.dat as RNA. Something else?
Then, as indicated in the tutorial, I paste the gro of the modified nucleotide into the gro file of the RNA.
Now I need to run pdb2gmx to obtain a topology of the whole complex, but I obtain the following error:
“Atom C5’ in residue PSU 54 was not found in rtp entry PSU with 14 atoms”
which is the first atom of modified nucleotide.
Going off of the tutorial, if you are starting with an RNA strand with known residues and then adding new ones yourself, it might be simpler to start with pdb2gmx on the known strand, then adding the modified nucleotides into the resulting topol.top along with the #include modified_nucleotide.itp line for defining the residues.
I’m not personally familiar with adding the .itp information directly into the cgenff.rtp file so can’t really advise on that, but my understanding is that the line in topol.top for including the forcefield is calling forcefield.itp which in turn calls ffnonbonded.itp and ffbonded.itp so those are the 2 files that need to be edited if you’re going to add the parameters directly (similar to how the parameters are added in KALP-15 in DPPC).