Hi everybody,<br>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:<br>
<br>Fatal error:<br>Residue numbers in the .top are not numbered consecutively from 1<br><br>I paste here my file .top:<br><br>; Include forcefield parameters<br>#include "ffG43a2.itp"<br><br>; Include chain topologies<br>
#include "a.complex_A.itp"<br>#include "a.complex_B.itp"<br>#include "a.complex_C.itp"<br><br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>
[ position_restraints ]<br>; i funct fcx fcy fcz<br> 1 1 1000 1000 1000<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>
; Name<br>Protein in water<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>Protein_C 1<br>SOL 28799<br><br>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.<br>
Does anybody know how can I manage to make grompp work?<br><br>Thank you in advance,<br>best regards,<br>Annalisa<br><br>-----------------------------------------------------<br>Annalisa Bordogna<br>PhD. Student <br>DISAT - Università degli Studi di Milano Bicocca<br>
Milano - Italy<br>-----------------------------------------------------<br><br>