[gmx-users] Protonation state: CYX HID

Jordi Camps jcamps at lsi.upc.edu
Mon Jun 13 18:28:30 CEST 2005 

> -----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 18:22
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Protonation state: CYX HID
> 
> 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?

Yes, I think so.

> 
> 
> 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
> > > >
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > ++++++++++
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the list. 
> Use the www 
> > > > interface or send it to gmx-users-request at gromacs.org.
> > > >
> > > > _______________________________________________
> > > > gmx-users mailing list
> > > > gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please don't post (un)subscribe requests to the list. 
> Use the www 
> > > > interface or send it to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > > --
> > > Kai Zhuang
> > > BioMedical Engineering @ University of Toronto kai dot zhuang at 
> > > gmail dot com kai.zhuang at gmail.com
> > > 6478314789
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the www 
> > > interface or send it to gmx-users-request at gromacs.org.
> > >
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the www 
> > interface or send it to gmx-users-request at gromacs.org.
> > 
> 
> 
> --
> Kai Zhuang
> BioMedical Engineering @ University of Toronto kai dot zhuang 
> at gmail dot com kai.zhuang at gmail.com
> 6478314789
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
--

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

More information about the gromacs.org_gmx-users mailing list