Dmitry Lupyan wrote:
Dear GROMACS Users,
I'm trying to use g_hbond (v4.0.3) to analyze a simulation which was
generated with NAMD (trajectory was converted to .trr w/VMD). The
g_hbond requires (i) a trajectory file, and (ii) a 'run input file'
(tpr/tpa/tpb). How do i generate this tpr/tpa/tpb file? Is there any
way I can use a plain PDB file for this?
No, you can't get away with a plain coordinate file. To identify the
atoms, an ordered mapping from the atoms in the .trr file to atom names
in a coordinate file would suffice, however g_hbond also needs a
description of the atomic connectivity. I guess that's so it can exclude
nearest-bonded-neighbour atoms from being observed withing H-bonding range.
There's no easy solution - you have to take a suitable coordinate file,
apply pdb2gmx, check the atom ordering is still the same, and then
supply it to g_hbond.
Mark
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