Dear Kushal, Regarding the first error, I feel that you have done a few mistakes while updating your topology section as your system has more atoms than what is in the topology. Kindly go through the tutorials on this site - http://www.mdtutorials.com/gmx/index.html, to get a picture on how to do it.
Regarding second error, I think your system has a ligand that the forcefield is not able to define. I am guessing you have already parametrized this. If you have submitted this ligand to a server, maybe you are using a different file than what you were supposed to? Kindly recheck. -- Regards, Prasanth. -- 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.
