Loading a Ecoli Ribosome structure in Gromacs 6i0y/4v7u

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GROMACS version: 2020.6-Debian-2020.6-2

I am trying to load the 6i0y structure in the Gromacs. I delete some of the parts by retaining the PTC region, and try to load in the gromacs I receive the error:

Fatal error:
Atom P in residue G 1 was not found in rtp entry RG5 with 32 atoms
while sorting atoms…

Making bonds…
Warning: Long Bond (48-50 = 0.331291 nm)
Number of bonds was 256, now 255
Generating angles, dihedrals and pairs…
Before cleaning: 667 pairs
Before cleaning: 677 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 677 dihedrals, 49 impropers, 462 angles
664 pairs, 255 bonds and 0 virtual sites
Total mass 1785.036 a.m.u.
Total charge 1.000 e
Writing topology
Processing chain 5 ‘A’ (61274 atoms, 2854 residues)
Identified residue G1 as a starting terminus.
Identified residue U2903 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.arn
Opening force field file /usr/share/gromacs/top/amber99.ff/dna.arn
Opening force field file /usr/share/gromacs/top/amber99.ff/rna.arn

Program: gmx pdb2gmx, version 2020.6-Debian-2020.6-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 745)

I tried running with different forcefields but end up with same issue. Am I doing something wrong as I find same issue in AMBER software.

Any help in resolving this issue would be really appreciated.
Thank you

2

Remove the phosphates (P, O1P, O2P) from the 5’-terminal end of nucleic acids, it’s neglected in most nucleic acid-specific force fields.

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3

Thank you this resolved my issue