Simply change the order of the atoms in the gro file to match the topology file.
The order of the atoms is not in itself what is important, ie they can really be in any order, it's that the names and order match between coordinate - topology file and then within the topology file. This error also typically shows up when the molecule list at the end of the topology is different to how the molecules are ordered in the coordinate file. For example coordinate file has 1x UNK, 1x SOL, 1x UNK then 3,000 SOL. A topology with a list of the molecules as 2x UNK then 3,001x SOL will throw up this error. On Thu, 11 Apr. 2019, 3:00 pm RAHUL SURESH, <drrahulsur...@gmail.com> wrote: > Hi Users. > > While doing protein-ligand simulation, I get a warning which state > atom name mismatch between solv.gro and topol.top and name from top file be > considered and gro will be ignored. Yes, there is a mismatch, as in gro > file, the atom was in the order C-O-O and in itp file added to top, the > order was O-C-O. the itp file was generated by prodrg server. > > 1. Is it fine to ignore the warning and continue with the simualtion? > > 2. If not, which file should i rename? gro or itp? > > > Thank you > -- > *Regards,* > *Rahul * > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.