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

[annalisa bordogna]

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?
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>

>
>
> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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