>> After editing the pdb only in the area of the names of the atoms (such as >> HB3), I was able to generate a topol.top file with a bond between the first >> nitrogen and the last carbon. However, I still have 2 too many hydrogens on >> the first nitrogen and 1 too many oxygens on the last carbon.
>You need to be using -ter and choosing "None" for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. >-Justin I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter " and was asked about the protonation states for two of the residues, but I was not asked about the termini. -Matthew -- 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.
