[gmx-users] itp file

[jozef hritz]

	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
> 
>