GROMACS version: 2019
GROMACS modification: Yes/No
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I am doing with GROMACS version 2019 and force field Amber99SB-ildn on complex of protein-DNA. In the parameterization for proteins, I use the command:
gmx pdb2gmx -f protein.pdb -p MOL_GMX.top -ignh -merge all -o MOL_GMX.pdb
It gives an error like the picture. Can someone tell me what’s wrong with my rtp file? and how to modify it? Thank you so much
The .rtp file contains the list of atoms that the forcefield has listed for the residue DT5, that an atom if not found in the rtp entry is more likely due to an extra atom being listed in the pdb file that shouldn’t be there, you might want to double check whether protein.pdb contains some error
I do with complex protein-DNA so residue DT is tyrosine nucleotide in DNA sequences and Atom P is phosphor atom of phosphodiester bond. I have checked in DNA.rtp but it is still declared atom P so until now i haven’t realized what is wrong?
When you checked the dna.rtp file, did all the atoms in DT 9 in the pdb file match all the atoms under DT5 in the rtp file (keep in mind that DT5 and DT are under different entries in the rtp file with DT5 being specifically for tyrosine nucleotides that are at the 5’ end of the dna strand)?
The nucleotide is thymine, not tyrosine (which is an amino acid).
Nucleic acids are typically not phosphorylated when in the 5’ position. Synthetic oligos sometimes are and that’s why they are in the structures. Remove phosphate atoms from 5’ and/or 3’ positions and try again.
omg thank you so much! I have realized my error and it was repaired.
