[gmx-users] Protonation state: CYX HID

[Kai Zhuang]

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.


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