Thank Neha ! I follow your advices but this error still appear. I don't know why.
By the way, does anybody know why there are not ions in topology file in Martini CG-MD. Because I see the system has not zero charge, i don't understand why the CG system not be neutralized by ions. Thanks and regards, KT On Fri, Jan 4, 2013 at 3:40 PM, Awasthi, Neha < [email protected]> wrote: > First check your .gro file and your .top file, to make sure atom 6518 (or > Water) is consistently defined. > > Next step would be to make sure this atom features in the index file > within a > "correct group". > In some cases, if a single atom is left out and not part of any group in > the > index file, it gives this error. > Why not make your index file again ? > Read the help provided with the command "make_ndx" to understand this. > Hope that works! > > -----Original Message----- > From: [email protected] on behalf of Kieu Thu Nguyen > Sent: Fri 1/4/2013 6:51 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] error with indexfile > Dear All, > > When using the command > grompp -f equi.mdp -c membedded.gro -p merged.top -n index.ndx -o > equilibrate.tpr > The error is > Fatal error: > Invalid atom number 6518 in indexfile > How can i fix this ? > Thank so much for any help ! > Regards, > KT > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
