Justin, I am not entirely sure I understand your sequence of steps. Why do you want to first run it normally, but then also without adding the hydrogens? The hydrogens (a total of two) are only added at the termini by default, and in the final product there's no need for them anyway.
Here's what I'm able to understand: run as usual, delete all bonded data relevant to termini, add bonded descriptions for the residues at the boundary, modify pdb to remove termini (actually, I can generate the periodic ones automatically). Am I missing something that should make my life easier? Also, is there a way to automate this by modifying the forcefield? See, right now (on the periodic structure without termini) pdb2gmx sees the first residue and looks it up as one with a terminus, which is really the gist of the error it throws, so I doubt it even gets to the point of looking at the boundary. Is it that the utility behavior cannot be changed at the ff level, and thus our only option is manual modification of the topology? Thank you, Alex JL> pdb2gmx isn't designed to intuitively handle such cases. The best way to go JL> about it is: JL> 1. Run pdb2gmx normally to add H that you might need and to apply patching such JL> that you have a phosphate on one end and an alcohol on the other (presumably you JL> already have this last part done and have suitable .tdb entries). JL> 2. Delete unnecessary atoms from the termini. JL> 3. Run pdb2gmx again with -ter (choose None) and -missing so that it doesn't JL> complain at you about dangling termini. JL> 4. Manually edit the topology to introduce the needed bond, angles, and dihedrals. JL> -Justin -- 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.
