Building topology for a modified RNA in complex with protein

User discussions
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GROMACS version:
GROMACS modification: Yes/No
Hi,
I have a strand of 15 RNA nucleotides that all have modifications, such as 2’F or addition of a methyl group, etc. I followed Justin Lemkul’s tutorial on parametrizing a new ligand (Protein-Ligand Complex) and treated each nucleotide as a ligand and parametrized them from scratch using antechamber, then converted the resulting Amber parameters to Gromacs topology and .gro files. Finally all the resulting topology files were added in the protein Gromacs topology and I built the complex topology and .gro files and followed the rest of tutorial with solvation, ionization.
All went well, except when I performed minimization I noticed that the bond between the P of one nucleotide and O3’ of the next nucleotide is broken. I suspect this is because each nucleotide was given a unique residue name and was treated as a separate entity, therefore there are no bonds between these separate units. The question is: what is the fastest way to solve this problem?
Thanks

2

Bonds do not break in molecular mechanics processes. If a bond is defined in the topology, it is there and always will be. If it elongates due to strain, that reflects a problem with the parameters. If you specify a bond in the .rtp entry between the present nucleotide and the next (e.g. O3' +P) then it will be part of the topology.

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Thanks Justin for your reply. The P-O3’ bonds were not included when I built the topology of the protein-modified RNA complex. My mistake was to parametrize every modified nucleotide like a ligand (following the protein-ligand tutorial mentioned above) and hence I now have 15 different .itp files (for each nucleotide) that were included in the topology of the complex like below:
; Include forcefield parameters
#include “amber99sb-ildn.ff/forcefield.itp”

; Include bases topology
#include “nt_atoms.itp”

; Include bases topology
#include “nt2.itp”
#include “nt3.itp”
#include “nt4.itp”
#include “nt5.itp”
#include “nt6.itp”
#include “nt7.itp”
And at the end of the complex topology I added:
[ molecules ]
; Compound #mols
Protein_chain_X 1
Ion_chain_B 1
PU 1
GFS 1
CMS 1
CF 1
CM 1
GM 1
AM 1
CM 1

My question is, how can I now include the P-O3’ bonds between the nucleotides? Is there a way to automatically generate the bonds between the nucleotides?
Or, should I change direction and instead add each modified nucleotide as a new residue following the relevant documentation? (Adding a Residue to a Force Field — GROMACS 2020 documentation) In that case how can I generate .rtp file formats for each modified nucleotide from antechamber output? since the acpype doesn’t seem to be generating the correct format and requires manual modifications that in the case of many new residues become unfeasible.

Thanks,
Zhaleh

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If you want the topology to be automatically built in a sensible way, you need to write .rtp entries. Standalone topologies for each new residue type do not do you much good.