[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 17:13:57 CEST 2009
Thank you VERY VERY VERY much, Justin!
I've done what you said and... Now it works!!!!!!
Cheers!
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, 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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