hi everybody, i am running Gromacs simulation with the protein 1f9b.pdb. I had earlier got some errors with the ligands present i.e FE, BCT and 3ID so i had run prodrg with BCT and 3ID but as prodrg server doesnot support for FE i had obtaine4d itp and top files for FE by pdb2gmx. and ommiting the HETATM portions i had obtained a gro file for 1f9b.pdb and later on had added the FE.gro , BCT.gro and 3ID.gro at the end of the 1f9b.gro file.then using pdb2gmx i got teh topology file which included the following at the end
; Include Position restraint file #ifdef POSRES #include "1f9b_with_ligand.itp" #include "FE.itp" #include "BCT.itp" #include "3ID.itp" #endif ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_A 1 FE 2 BCT 4 3ID 15 SOL 27303 but while running the grompp step i am getting error Fatal error: No such moleculetype FE i tried to move FE to another column like ions but thyen i get the same error with BCT and 3ID. Any suggestions are highly appreciated.
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