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

[Justin A. Lemkul]

annalisa bordogna wrote:
> 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"
> 
> #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 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?
> 

The problem actually pertains to (at least) one of the chains you've included. 
Numbering is inconsistent in that file.  Check the .itp files and make sure the 
atoms are numbered consecutively.

-Justin

> Thank you in advance,
> best regards,
> Annalisa
> 
> -----------------------------------------------------
> Annalisa Bordogna
> PhD. Student
> DISAT - Università degli Studi di Milano Bicocca
> Milano - Italy
> -----------------------------------------------------
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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