I have modelled a custom RNA sequence into a 3D structure and now I want to simulate it using molecular dynamics. It is not capped and contains a free phosphate group attached to the first nucleotide at the 5’ end. I am using Gromacs 2022.3 version. When I try to build the topology file this error shows up: Atom P in residue A 1 was not found in rtp entry RA5 with 31 atoms while sorting atoms. I have tried using the ‘–ter’ option in the pdb2gmx command also, the same thing shows up.
What to do?
Thank You in advance.
Nucleotides aren’t typically phosphorylated at the 5’ end, try removing the phosphate group from the file
Thank you for the help.
Would there be no potential problem with removing the phosphate atoms? For instance, incorrect modelling of the biological reality, change in the overall actual charge of the RNA. Further, would it not affect the flexibility pattern study using the MD simulation data?
You should tell us what the biological reality of your problem is :) In some rare cases (like around the nucleolytic cleavage of a chain), the 5’ phosphate will be absolutely crucial and you’ll have to add a residue template for it, there are ways to do that. In 90%+ of situations, though, the 5’ terminus is either far enough from everything else not to matter much, or actually not phosphorylated in the real molecule you’re trying to model. Hard to tell without more information - there’s no “one-size-fits-all” RNA, as RNAs in living cells are usually produced by quite some processing and maturation. For synthetic RNAs, you might need to consult your (lab’s) protocol. But again, often it just won’t matter for your particular question.