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

Marysa van den Berg mvdberg1986 at hotmail.com
Thu Jan 28 19:16:19 CET 2010



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"



; Strong po

sition restraints for InflateGro


#include "strong_posre.itp"



; Include DPPC chain topology

#include "dppc.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



[ 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?




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