[gmx-users] Protonation state: CYX HID

[Kai Zhuang]

On 6/13/05, Kai Zhuang <kai.zhuang at gmail.com> wrote:
> thx for the replies.
> 
> i'm using Gromos96 43a1 right now.
> 
> what's the difference in hydrogen names?
> 
> cuz i get this error as well:
> Fatal error: Atom HD1 in residue HISB 8 not found in rtp entry with 12 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.
>>>for this i just removed all hydrogens in DeepView and let pdb2gmx
to add all the hydrogens for me.  that works right?
> 
> On 6/12/05, Jordi Camps <jcamps at lsi.upc.edu> wrote:
> > Hello,
> >
> > This names make me remember the names that AMBER uses to name some residues.
> > I found that some residues have different names, and a small conversion
> > table is this:
> >         AMBR/GMX
> >         ---------
> >         HID /HISA
> >         HIE /HISB
> >         HIP /HISH
> >         ASH /ASPH
> >         CYX /CYS2
> >         CYS /CYSH
> >         LYS /LYSH
> >         HEM /HEME
> >         NME /NAC
> >
> > You will have to change the residue names and probably the hidrogen atom
> > names too. Which force field are you using?
> >
> > --
> > Jordi Camps Puchades
> > Instituto Nacional de Bioinformatica (INB) Nodo Computacional GNHC-2
> > UPC-CIRI
> > c/. Jordi Girona 1-3
> > Modul C6-E201                     Tel.  : 934 011 650
> > E-08034 Barcelona                 Fax   : 934 017 014
> > Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu
> >
> > -----Mensaje original-----
> > De: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] En
> > nombre de David
> > Enviado el: domingo, 12 de junio de 2005 10:23
> > Para: Kai Zhuang; Discussion list for GROMACS users
> > Asunto: Re: [gmx-users] Protonation state: CYX HID
> >
> >
> > 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.
> > ________________________________________________________________________
> > 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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> 
> 
> --
> Kai Zhuang
> BioMedical Engineering @ University of Toronto
> kai dot zhuang at gmail dot com
> kai.zhuang at gmail.com
> 6478314789
> 


-- 
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789