I am using Gromacs 2020.4 for MD simulation study of yeast t-RNA (PDB ID- 6TNA) but the force field parameter file(rna.rtp) does not have CM atom charge values for adenine and guanine atom types. Because of it, error message is coming during pdb2gmx command. If anyone have any idea how can I get the charge values of it. Please do reply.
Thanks in advance
Hi, does the CM atom belongs to HETATM or is it G (10.A)? If it is heteroatoms, you need to parametrize the charges using any quantum method or find a previously published article where the authors did the parametrization, and ask them to provide you with charges (or the entire topology file).
I think it is just the usual Nucleic acid, and if you agree, you can rename the atoms (and even residues) to match the atoms types in FF and then run pdb2gmx.
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