[gmx-users] Protonation state: CYX HID

David spoel at xray.bmc.uu.se
Sun Jun 12 10:22:46 CEST 2005

On Sat, 2005-06-11 at 21:06 -0400, Kai Zhuang wrote:
> hi,
> I'm simulating a system that include the HETATM groups: CYX and HID
> pdb2gmx seems to have trouble with the protonation state that they are in.
> i did:
> /usr/local/bin/pdb2gmx -f ZKH-001-001-001.pdb -p ZKH-001-001-001.top
> -o ZKH-001-001-001.gro -merge
> and got error: 
> Fatal error: Atom HB2 in residue CYS 3 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.
> then i tried with -ignh tag to ignore the hydrogens, got new error:
> Warning: 'HID' not found in residue topology database, trying to use 'HIS1'
> how should i edit the pdb file?
see if the groups you want are present in the rtp file under another
name. then use that name. if they are not then you'll have to make one.
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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