[gmx-users] No such moleculetype FE

Sonali sonalipriyadarshini at gmail.com
Mon Apr 30 11:23:10 CEST 2007

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"

; Include water topology
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; 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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