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? Thank you in advance, best regards, Annalisa ----------------------------------------------------- Annalisa Bordogna PhD. Student DISAT - Università degli Studi di Milano Bicocca Milano - Italy -----------------------------------------------------
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