Hello Mark Sir, I have tried that way also. The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p topol.top -o box_pr.tpr But this time i get an error like this "Atom 1 defined in multiple groups (1 & 3). " How to overcome this error ?
Thanking you, Pawan On Thu, Apr 9, 2009 at 10:14 AM, Mark Abraham <[email protected]>wrote: > Pawan Kumar wrote: > >> Hello sir, >> >> Thanks for such a explanatory tutorial. >> I am stuck with one error now. >> I have protein, popc, sol and cl- in my system. >> I have merged the sol and cl- using make_ndx. >> But when I run grompp I get the error like this "popc not defined in the >> index file". >> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o >> box_pr.tpr >> > > As I said last time, you'll need to give grompp the index file so that it > can make sense of your use of the new group(s) name(s). > > Mark > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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