[gmx-users] protein covalently bond to ligand

hazizian hazizian at razi.tums.ac.ir
Fri Jul 3 09:03:07 CEST 2009

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?
Tehran University of Medical Sciences

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