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I am new to GROMACS and is using the same for trajectory analysis. I have phosphoserine and phosphothreonine generated in charmm36 ff. While running pdb2gmx I am getting the error ‘Atom PL in residue THR 114 was not found in rtp entry THR with 14 atoms while sorting atoms’. I have edited the charmm .rtp, atomtypes.atp and residuetypes.dat to include corresponding atom types.
Atom names must match what is defined in the .rtp entry corresponding to that residue. Correct the atom names in your coordinate file.
Hello,
Were you successful? I am experiencing the same problem and am unable to continue. I am working with the SER184 residue to which I add an acyl donor to this residue.