[gmx-users] special molecule

Dongsheng Zhang dong at pampas.chem.purdue.edu
Mon Jun 12 17:25:54 CEST 2006

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!


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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