GROMACS version: 2018.3
GROMACS modification: No
I’m completely new to this but is GROMACS usable if I am trying to model the self-assembly of three molecules (one long-chain omega hydroxy fatty acid, glycerol, one phenolic acid) in a given solution? No proteins at all. I am following the Lysozyme tutorial (force field OPLS-AA/L, water TIP4P TIP 4-point) but get fatal error after running
gmx pdb2gmx -f file.gro -p file2.top -ignh
Fatal error:
Residue ‘C’ not found in residue topology database
and after grompp this error:
Fatal error:
number of coordinates in coordinate file (fgjc1_solvv.gro, 3149) does not match topology (topol.top, 40104)