[gmx-users] SEP and HO atom type

[David]

On Tue, 2003-02-04 at 22:03, Luciane Vieira de Mello wrote:
> Dear Anton,
> 
> Thanks for you help.
> I got your two mails, but unfortunately I haven't managed to solve the
> problem yet.
> What exactly should I do in order to have the HO atom type when I run
> grompp?
> In fact I have used :
> 
> [phospho]$ pdb2gmx -f phosphoserine.pdb
> 
> choose the new option:  number 5
>  0: Gromacs Forcefield (see manual)
>  1: Gromacs Forcefield with all hydrogens (proteins only)
>  2: GROMOS96 43a1 Forcefield (official distribution)
>  3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
>  4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
>  5: ffG43a1 with SEP, TPO and PTR
> 
> and chose ffG43a1 with SEP, TPO and PTR for pdb2gmx,
> 
> Why should grompp not work when pdb2gmx was fine?  grompp is working with
> the output of pdb2gmx! (.top)
> 
Because the rtp defines an atom that is not in the itp files of the
force field. However, HO is a normal alcohol hydrogen that should be in
there. Check the definitions of SEP etc. in your rtp file and compare
them to the itp file. Do also look in your top file to see whether atom
names have been translated appropriately into atomtypes. 

> thanks in advance
> 
> +-------------------------------------------------------------------------+
> |                  Dra. Luciane Vieira de Mello Rigden                    |
> | e-mail: mello at cenargen.embrapa.br                                       |
> | Embrapa Recursos Geneticos e Biotecnologia                              |
> | Parque Estacao Biologica           |  http://www.cenargen.embrapa.br    |
> | PqEB - Final - Av. W3 Norte        |  Phone:  +55 (61)448-4741          |
> | 70770-900, Brasilia-D.F.-BRAZIL    |  Fax:    +55 (61)340-3658          |
> +-------------------------------------------------------------------------+
> 
> 
> 
> On Tue, 4 Feb 2003, Anton Feenstra wrote:
> 
> > Luciane Vieira de Mello wrote:
> > [...]
> > > I am not sure if I am checking the right file:
> > > ffG43a1nb.itp
> > > where I tried to add the HO atomtype from ffgmx2nb.itp, including the
> > > pairtypes.
> >
> > There is also a .atp file (for Atom TyPes), but IIRC that is only
> > used by pdb2gmx and not grompp... ;-(
> >
> >
> > --
> > Groetjes,
> >
> > Anton
> >   ________ ___________________________________________________________
> > |        | Anton Feenstra                                            |
> > | .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
> > | |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
> > | |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
> > | ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
> > |  /  \  |-----------------------------------------------------------|
> > | (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
> > |  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
> > |   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
> > |  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
> > | (    ) |-----------------------------------------------------------|
> > |  \__/  | "If You See Me Getting High, Knock Me Down"               |
> > |        | (Red Hot Chili Peppers)                                   |
> > |________|___________________________________________________________|
> >
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> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
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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