[gmx-users] special molecule

[Alan Dodd]

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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