> 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?
Not at all, as demonstrated by ... > 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 !!!!!! You removed the .itp that specifies water, spc.itp, so it is not surprising that it no longer knows what SOL is. > How can I fix these problems ????????????????? Have a look at http://www.gromacs.org/index.php?title=Documentation/Error down the page in the grompp section the original error you came across is dealt with. Catch ya, Dr. Dallas Warren Department of Pharmaceutical Biology Pharmacy and Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. _______________________________________________ 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