[gmx-users] No molecules were defined in the system/ No such molecule type Dio

[sarah k]

Dear all,

I'm trying to simulate several drug-protein complexes on a clustered
server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files.
Here is the final lines of my .top file:



; Include Position restraint file

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif



; Include water topology

#include "spc.itp"



; Include Dio topology

#include "dio.top"



#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

Nona in water



[ molecules ]

; Compound        #mols

Protein_X           1

Dio                 1

SOL             63598





The statements are closed with #endif. Yet I recieve "No molecules were
defined in the system". For the same file I sometimes get "No such molecule
type Dio" in the first grompp prompt. What's the solution?



Regards,

Sarah Keshavarz