Dear Yaser, Gro file is sensitive and you should update the number manually after adding the ligand atoms to the protein.gro file. Check the first line of your protein.gro and ligand.gro. In the complex.gro the first line should be the summation of both. Gromacs does not perform it manually. Kindly chck again and rerun the grompp.
Good luck Bikash Osaka On Wednesday, December 17, 2014, Yaser Hosseini < yaser.hosseini.biolog...@gmail.com> wrote: > hi gromacs users > > i got error in step four in protein-ligand complex how can i fix it: > > Fatal error: > number of coordinates in coordinate file (solv.gro, 144131) > does not match topology (topol.top, 144171) > > when i want to ran this: > > grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr > > i add my ligand drg.gro in protein_processed.gro. > > beside i cant find conf.gro that you say in this toturial: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/02_topology.html > > thank you . > -- > 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 <javascript:;>. > -- Warm regards Bikash Ranjan Sahoo Sent from I Phone 5 Osaka, Japan -- 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.
