GROMACS version: 2020
GROMACS modification: No
I want to start a dynamic simulation for a protein that contains “Iron-Sulfur Cluster” using gromacs 2020, and I do not have the force field parameters for this groupement;
I got this message “Residue ‘FES’ not found in residue topology database”
and I am using “charmm36-feb2021.ff” for the atoms force field parameter. Could you please provide me with the force field parameters of the FES group.
I am a beginner and I don’t know how to get the parameters from published papers;
I need the code like this to add it to merged.hdb file:
HEME 16
1 1 HA CHA C1A C4D
1 1 HB CHB C4A C1B
1 1 HC CHC C1C C4B
1 1 HD CHD C1D C4C
3 4 HMA CMA C3A C2A
2 6 HAA CAA C2A CBA
2 6 HBA CBA CAA CGA
3 4 HMB CMB C2B C1B
1 1 HAB CAB C3B CBB
2 3 HBB CBB CAB C3B
3 4 HMC CMC C2C C1C
1 1 HAC CAC CBC C3C
2 3 HBC CBC CAC C3C
3 4 HMD CMD C2D C1D
2 6 HAD CAD C2D CBD
2 6 HBD CBD CAD CGD
but for FES not for HEME,