[gmx-users] itp file

[Daan van Aalten]

Dear Jozef

The "GROMACS philosophy" towards making small molecule topologies is
implemented in PRODRG. 7-membered rings (as 3,4,5,6,8+ membered rings)
are no problem. PRODRG will automagically choose the most suitable atom
type, bond lengths, angles etc etc.
See
http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html


Daan

On Tue, 19 Feb 2002, jozef hritz wrote:

> 	Dear Erik,
> I would like to ask again for force field parameters, because I don't
> have problem with some missing parameter, but I am not sure which
> parameters are taken in simulation. I have small ligand which contain also
> some atipical parts, e.g. 7-ring. In itp file I used for these carbons CR6
> or CB atom type and defined charges, all bond, angle and dihedral
> parameters. But during simulation lincs crash down and structure looks
> horrible. It is reason why I am asking when in top file are included
> ffgmx.itp (I need it for protein) as well as newmolecule.itp what
> parameters are taken in simulation e.g. for dihedrals and what
> parameters for L-J potential which are not in newmolecule.itp
> 
> 	Thanks
> 								Jozef
> 
> 
> > > I would like to ask for 'gromacs philosophy' from the point of itp file.
> > > On the 97th page in gromacs manual is described urea.itp file.
> > > It contains atom types and some parameters (e.g. bonds), but don't have
> > > contain all needed.
> > >
> > > top file looks like:
> > > #include "ffgmx.itp"
> > > #include "urea.itp"
> > >
> > > Does it mean that for defined parameters in urea.itp they are taken into
> > > account (has urea.itp higher priority like ffgmx.itp?) and others
> > > (missing in urea.itp) are contructed on the base of atom types(defined in
> > > urea.itp) from ffgmx.itp?
> > 
> > We simply use the C preprocessor, so it is equivalent to copying the whole
> > contents of each included file instead of the include-statement.
> > 
> > You can use it any way you want, but by default we have one include for the
> > forcefield used (ffgmx) and then an include for each molecule from the
> > library. The molecules depend on the forcefield of course, but usually not
> > the other way around :-)
> > 
> > Don't worry too much about it, you'll get warnings about undefined or
> > redefined stuff I think :-)
> > 
> > Erik
> > 
> > 
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

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