I am using pdb2gmx to generate topology files for KRASG12C which is GDP bound but I am getting this error “the residues in the chain mg301–gdp302 do not have a consistent type. the first residue has type ‘ion’, while residue gdp 302 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 residue types.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.” can you give a step-by-step solution as I am new to this field?
Related topics
Topic | Replies | Views | Activity | |
---|---|---|---|---|
Issue in generating topology files for protein with GDP residue | 0 | 38 | December 4, 2024 | |
Error while running writing the topology | 2 | 448 | June 18, 2024 | |
Pdb2gmx - "This chain does not appear to contain a recognized chain molecule." but ion is in the FF | 2 | 2117 | September 14, 2021 | |
Error while generating the topology by gmx pdb2gmx | 1 | 444 | November 2, 2023 | |
Fatal errors | 0 | 441 | March 1, 2023 |