[gmx-users] protein-protein complex

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 3 13:44:46 CEST 2007

Hi Fulya,

If your ligand is a protein, then use pdb2gmx!
There's nothing special with 'being a ligand', and it's certainly not
required to run it through PRODRG, because someone decided that part
was to be called ligand, whereas the other part was not.


On 7/3/07, fulya caglar <fulyacaglar at yahoo.com> wrote:
> Hi  all !
> We want to MD simulation of a protein-protein complex.We can't prepare itp.
> and gro files with PRODRG server.Because there are too many atoms in my
> ligand (which is a protein). How can we prepare the .itp and .gro files?Are
> there any tutorial for a protein protein complex?
> Best Regard
>  Fulya
> Hacettepe University
> Turkey
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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