[gmx-users] pdb2gmx - generating hydrogens

Vladimir Nesterov Vladimir.Nesterov at gmx.net
Mon Dec 26 12:00:52 CET 2005


I was wondering if anybody knows, which hydrogens are generated by pdb2gmx
and by means of which system. It seems to me that only H-atoms are added,
which are included in the residue topology file, where aryl H-atoms are all
omitted, whereas polar H-atoms are contained. Why?

I am asking, because I tried a simulation of a protein structure that was
determined with NMR (and nearly all hydrogen-positions are known) and
pdb2gmx produced following error:

Fatal error: Atom HA in residue CYS2 1 not found in rtp entry with 7 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

But using -ignh all H-atoms are removed and only a few are generated and I
lose a lot of positional information. The only solution I found was to use
-ignh and then generate the missing H-atoms with protonate (but then I have
to edit the whole topology). Does anyone know how to handle this?

Thank you very much & best regards,
Vladimir Nesterov

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