[gmx-users] special molecule

[Tamas Horvath]

So if I generate an .itp with PRODRG, and link it in the .top file, then
grompp can use the original .pdb file? Or it's not that simple?

On 6/12/06, Alan Dodd <anoddlad at yahoo.com> wrote:
>
> It's entirely possible to mix and match forcefield
> files to create a hybrid forcefield - the lipid
> forcefield I use has OPLS parameters for the
> headgroups, custom parameters for lipid tails, and GMX
> parameters for everything else.  As long as the hybrid
> forcefield is internally consistent, it will work.
> How accurate it is, is another matter...
> So yes, you can technically use PRODRG itps with other
> forcefields, but bear in mind firstly, atomtypes etc
> in your itp file will all need checking to make sure
> they are accounted for in both forcefields (are
> 'default' values the same in one forcefield as
> another, for instance?  Probably not - you may need to
> alter the itp to describe defaults explicitly), and
> secondly that they are not designed to be used in the
> same system.
>
> --- Dongsheng Zhang <dong at pampas.chem.purdue.edu>
> wrote:
>
> > Sear Mark,
> >
> > Since PRODRG server only generates a itp file by
> > using gromos type force
> > field, do I have to use gromos force field for my
> > whole protein-ligand
> > system if my ligand force field parameters are got
> > from PRODRG? In
> > another word, can I mix two different force field
> > (one for protein, one
> > for ligand) in one system? Thanks!
> >
> >
> > Best Wishes!
> >
> > Dongsheng
> >
> >
> >
> > On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham
> > wrote:
> > > Tamas Horvath wrote:
> > > > As I understand, if there are "special"
> > molecules in a pdb file, pdb2gmx
> > > > cannot convert it. However, PRODRG can create an
> > *.itp file for that
> > > > molecule, so that I can include it in the
> > generated topology file. But
> > > > how can I place the molecule in it's original
> > position? Or even better,
> > > > how can I convert the original ("full") .pdb
> > file for gromacs?
> > >
> > > Where's the problem? pdb2gmx makes a .top file for
> > your non-special
> > > system, you #include the .itp file for your
> > special part. There's
> > > nothing about atomic positions yet.... have a look
> > at a .top file. Now
> > > grompp takes the .top and some file with atomic
> > positions and makes a
> > > .tpr file. Same general procedure as normal.
> > >
> > > Mark
> > > _______________________________________________
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