Hi,
Building whole capping groups has never been in scope for pdb2gmx, and
particularly not for the AMBER force fields, which use specially
parameterised charged amino acid termini (for example). IIRC there are also
some neutral capping groups in .rtp files that are usable as residues, but
pdb2gmx
Hello again
I have noticed that in case of the amber* forcefields (in gromacs v504) the
aminoacids.n.tdb and aminoacids.c.tdb files are empty* so it is not possible to
construct easily a capped AA with the pdb2gmx -ter command without using a rtp
file (and it is very painful). So does anyone ha
