[gmx-users] SEP and HO atom type

[Luciane Vieira de Mello]

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)

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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