[gmx-users] grompp gives "no molecules were defined in the system"

[Marysa van den Berg]

Hi,

 

The number of atoms in the second line of my .gro file are correct, I checked that.

 

This is what my topology file says in the beginning:

 

[ moleculetype ]

; Name      nrexcl

Protein      3

 

No changes here after the solvation.

 

At the end after the [ atoms ] directive:

 

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

 

; Strong po

sition restraints for InflateGro

#ifdef STRONG_POSRES

#include "strong_posre.itp"

endif

 

; Include DPPC chain topology

#include "dppc.itp"

 

; Include water topology

#include "spc.itp"

 

#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

Protein

 

[ molecules ]

; Compound #mols

Protein        1

DPPC          242

SOL           48333

 

The only thing in the topology that changed after the solvation, was adding the watermolecules in the [ molecules ] section (SOL 48333)

What could be the problem?

 

Thanks,

 

Marysa
 		 	   		  
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