Dear All, when I want to use grompp program grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o minimbrady.tpr
I got the following error message Fatal error: [ file "spc.itp", line 41 ]: Atom index (1) in settles out of bounds (1-0) So I tried to modify the topology file by removing the following ; 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" Since there is no needs also ions.itp , because I didnot add any ions to the structure. Is this right? Finally, I tried to use grompp again with the modified topology file. I gety a different error message Fatal error: No such moleculetype SOL I donot know why SOL (water) didnot recognized by grompp !!!!!! How can I fix these problems ????????????????? Regards, Asmaa_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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