GROMACS version: 2022
GROMACS modification: No
“Atom OP3 in residue G 1 was not found in rtp entry RG5 with 32 atoms
while sorting atoms.”
How do I deal with this error?
Remove any phosphate group from terminal residues; these are often present synthetically but are not how force fields are typically parametrized (5’-OH terminus is typical).
Could you kindly elaborate? Would honestly mean a lot.
Regards,
Chandraniv
Nucleic acids typically do not have 5’-phosphate groups. Force fields are parametrized to the most common use cases and do not necessarily cover all possible chemical space. Delete the phosphate atoms from the 5’-nucleotide and you can generate the topology such that it has a free 5’-hydroxyl group.
Good day, if it still actual:
With the free AmberTools you can prepare .gro and .top files, which can be handled by GROMACS.
Recent amber force fields have pretty interesting modification: they can work with terminal phospate residues. In Amber23 manual written that you need to change OP3 residue type into OHE (Check p. 43).
More about converting PDB to amber files and then to GROMACS can be find in Amber23 manuals (p. 308). In manual it is written for RNA, but in my case it work well with DNA fragment