@ Mark, i added -ter to pdb2gmx command and produced the topology file but still the energy minimization step in vacuum is producing the same error
@justin am presently running the simulation step i.e energy minimization of structure in vacuum. when producing the topology file ,it gave errors saying some of the atoms are missing in atomtypes which i gave , you said atoms shouldn't be added which were not in the first place then can u tell me the alternative. regards ram -- View this message in context: http://gromacs.5086.n6.nabble.com/Fatal-error-Atomtype-O2-not-found-tp4998254p4998261.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
