[gmx-users] Protonation state: CYX HID

[Jordi Camps]

Hello,

You can choose to let pdb2gmx put the hidrogens for you. This is achieved
with the -ignh command line parameter.
If you need to conserve the hidrogens with their positions and/or
velocities, then you should look for the name equivalences. If your original
files have all the atoms, some of them must be stripped, because G43a1 is a
unified force field, which means that some hidrogens are "unified" with the
heavy atom to which they are bonded.
You can try to compare the original file with the resulting file using -ignh
to see the differences in nomenclature.

--

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 Kai Zhuang
> Enviado el: lunes, 13 de junio de 2005 17:24
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Protonation state: CYX HID
> 
> 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
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