[gmx-users] No such moleculetype FE

Venky venky.agas at gmail.com
Mon Apr 30 11:45:59 CEST 2007

On 4/30/07, Sonali <sonalipriyadarshini at gmail.com> wrote:
> 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

You have included the topology files inside a IF function,,, unless you
define -DPOSRES in your grompp those include files won't be read. So the
cause of the error... place the  FE, BCT and 3ID include lines out of the IF
statement (which starts with #ifdef and ends with a #endif)
I don't see a reason why you would put the include lines inside the IF
statement. In case you are trying to do a position restrained MD, you need
to list all the BCT, 3ID and FE atoms and the force with which you want to
restrain them in the posre.itp file.

; Include water topology
> #include "spc.itp"
> ; 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.


~ You will become rich and famous, unless you don't.
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