[gmx-users] Grompp fatal error (Residue numbers in the .top are not numbered consecutively from 1)

annalisa bordogna annalisa.bordogna at gmail.com
Mon Apr 6 16:38:23 CEST 2009

Hi everybody,
I am setting up an MD run on a peptide-protein complex with gromacs. I have
defined the box and solvated the system, but now I'd like to equilibrate the
solvent, so I tried with grompp, but an error occurs:

Fatal error:
Residue numbers in the .top are not numbered consecutively from 1

I paste here my file .top:

; Include forcefield parameters
#include "ffG43a2.itp"

; Include chain topologies
#include "a.complex_A.itp"
#include "a.complex_B.itp"
#include "a.complex_C.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
Protein in water

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
Protein_C           1
SOL             28799

I have searched in the wiki and in the archives of the mailing list, but I
have found no hints on how I could fix it.
Does anybody know how can I manage to make grompp work?

Thank you in advance,
best regards,

Annalisa Bordogna
PhD. Student
DISAT - Università degli Studi di Milano Bicocca
Milano - Italy
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