[gmx-users] pdb2gmx - generating hydrogens

David van der Spoel spoel at xray.bmc.uu.se
Mon Dec 26 14:31:27 CET 2005

Vladimir Nesterov wrote:
> Hello,
> 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?
depends on force field. for gromos only polar hydrogens are present. 
opls has all hyrdogens.
you may nevertheless be force to use -ignh because there are 4 different 
naming schemes for Hs in practical use. Only if you have exactly the 
same as gromacs can you use the existing positions.

> 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

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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