Can I import pdb files with some or all hydrogens missing (-ignh flag)?
Yes and No. Protein ports have working hydrogen database (.hdb) files in all versions of our ports, so it is not necessary to have all-atom pdb models (i.e. including hydrogens). It is essential to copy aminoacids.dat to the top directory for this feature to work properly. Hydrogen databases are also present for nucleic acids in GROMACS versions 3.3 ports, but this feature was not plausible in previous versions of pdb2gmx, which makes 3.3 a nice improvement for those simulating nucleic acids. For nucleic acid simulations in versions 3.1.4 and 3.2.1 all-atom pdb models are still needed (i.e. united atom models will need to be protonated ahead of time using outside software).
