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

[Justin A. Lemkul]

annalisa bordogna wrote:
> Hi, Justin,
> thank you for your reply.
> I have just checked my .itp files.
> I have 7 itp files:
> - one is generated by doing genpr to define the restraints on the protein;
> - six (two for each chain of my complex) are generated directly by 
> pdb2gmx (first step of my simulation).
> 
> The first itp file is ok: numbers are consecutive and starting from1.
> The other six files have not consecutive numbers (I paste here the first 
> lines of one of these files):
> 
> [ position_restraints ]
> ; atom  type      fx      fy      fz
>      1     1  1000  1000  1000
>      4     1  1000  1000  1000
>      5     1  1000  1000  1000
>      6     1  1000  1000  1000
>      7     1  1000  1000  1000
> 
> Since they are automatically generated by pdb2gmx, how can I fix the 
> problem?

Let's go back to the original problem (which should not be related to the 
position restraint files; they will not be numbered consecutively).  The error 
message states that the residue numbers are not numbered consecutively from 1. 
Your problem is coming from residue numbering, not atomic numbering (apologies 
for my typo in the last mail).

So you need to be examining the chain topologies and structure files to make 
sure that the numbering matches up, and begins with 1.

-Justin

> Thank you very much.
> 
> Annalisa
> 
> -----------------------------------------------------
> Annalisa Bordogna
> PhD. Student
> DISAT - Università degli Studi di Milano Bicocca
> Milano - Italy
> -----------------------------------------------------
> 
> 
> 
> 2009/4/6 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     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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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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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

========================================