Errors in generating topology for RNA with unnatural residues

User discussions
1

GROMACS version:2019
GROMACS modification: No
Here post your question
Hello all,
I want to simulate a pre-initiation complex containing 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. which has unnatural residues such as 2MG(2-Methyl Guanosine), 1MG,(1-Methyl Guanosine) 1 in it and whenever I try to run the pdb2gmx program to generate the topology and the Gromacs compatible coordinates , I get following error:
The command: gmx pdb2gmx -f 3jaq_004.pdb -o 3jaq_004.gro -ter
Force Field : CHARMM36-MAR2019, Water Model: TIP3P
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier ‘2’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier ‘C’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier ‘Q’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier ‘k’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 49 chains and 0 blocks of water and 8172 residues with 88831 atoms

WARNING: there were 0 atoms with zero occupancy and 1 atoms with
occupancy unequal to one (out of 88831 atoms). Check your pdb file.
Fatal error:
The residues in the chain ADE1–ADE76 do not have a consistent type. The first
residue has type ‘RNA’, while residue 1MG9 is of type ‘Other’. Either there is
a mistake in your chain, or it includes nonstandard residue names that have
not yet been added to the residuetypes.dat file in the GROMACS library
directory. If there are other molecules such as ligands, they should not have
the same chain ID as the adjacent protein chain since it’s a separate
molecule.

I tried by converting this .pdb file to .gro file format using gmx editconf and using that .gro file in pdb2gmx program which seems to read the file but then again with lots of warning as similar to “he first
residue has type ‘RNA’, while residue 1MG9 is of type ‘Other’”.
Do kindly help me out.

Regards,
Pallav Sengupta,
PhD Student,
Computational Biology Lab,
IIT Guwahati, Assam, India.

2

Adding to it I did copy the CHARMM36 force field to my local directory and called the force field from there, and also have added these unnatural residues such as 2MG, 1MG etc to my residues.dat file in my local directory and have called it while using the pdb2gmx with -ff option.

3

The solution that worked out for me was: modifying the residuetypes.dat file in the global directory of GROMACS by adding those modified residues and specifying them as RNA.
The other way out should be copying the samefile in the local directory and specifying the path for the residuetypes.dat file so that the this particular file is read from the local directory.

4

Can you tell me…how to specify the path for aminoacid.dat file?

1 Like