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

sarah k dailycolors at gmail.com
Wed Sep 12 07:58:57 CEST 2012

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"


; Include water topology

#include "spc.itp"

; Include Dio topology

#include "dio.top"


; 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

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?


Sarah Keshavarz

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