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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