[gmx-users] Protonation state: CYX HID
Kai Zhuang
kai.zhuang at gmail.com
Mon Jun 13 18:21:35 CEST 2005
thx for the scripts man.
i'll try them tonight and give you some feedback =-)
i stripped the hydrogens with "Remove Hydrogen (all)" command in Deep View.
which means i'm sending pdb2gmx a pdb file with no hydrogen atoms, which
is the equivalent of -ignh in this case right?
On 6/13/05, Jordi Camps <jcamps at lsi.upc.edu> wrote:
> 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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--
Kai Zhuang
BioMedical Engineering @ University of Toronto
kai dot zhuang at gmail dot com
kai.zhuang at gmail.com
6478314789
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