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 <jalem...@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 <jalem...@vt.edu <mailto:jalem...@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 >> ----------------------------------------------------- >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> 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 >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > 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@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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