Hi I want to do MD with a protien with prydoxal phosphate(PLP) which attache covalently to one lysine. For this I extract the Toplogy of lysine-PLP from PRODRG server.(DRGGMX.ITP and DRGPOH.PDB).I Changed the name DRGGMX.ITP to DRG.itp. after donig pdb2gmx -f m.pdb -o m1.pdb -water spce with the protein without PLP (m.pdb=protein whitout covalent bond) , I modified the topol.top file followig this: 1- add "DRG.itp" under the forcefield section on topol.top 2- add "DRG 1" under the molecule sectin of topol.top also I modifed m1.pdb: cut the related lysine (LYS 360) in the m1.pdb and paste the modified lysine- PLP (DRG 360)coordination from DRGPH.PDB. then I do editconf -f m1.pdb and genbox -f m1.pdb successfully, but when I want to do grompp the following fatal error appeared: There is no DRG moleculetype. what should I do now? Thanks. -- Tehran University of Medical Sciences www.tums.ac.ir
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