[gmx-users] special molecule

[Florian Haberl]

Hi,

On Monday 12 June 2006 17:25, Dongsheng Zhang 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!

Mixing ff types is a bad idea, i don`t know if PRODRG supports other ff like 
the old and depracted gmx format.

I hope that there will be soon a PRODRG version which will support other force 
field formats, also amber ff in gromacs without heavy modifing the pdb file.

As a hint: Take a look at 
http://www.gromacs.org/gromacs/documentation/tutorial.html

for builing a system of ligand and protein.

>
>
> 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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Greetings,

Florian

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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