[gmx-users] Protonation state: CYX HID

Jordi Camps jcamps at lsi.upc.edu
Mon Jun 13 01:00:13 CEST 2005


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:
        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
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 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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