[gmx-users] Protein - Ligand simulation

lucaam86 borroluca at gmail.com
Tue Feb 11 20:20:38 CET 2014

Hi, I'm not a Biologist, I'm designer interested to molecular modelling and
3D visualization of proteins and molcules.
I use gromacs but I'm not an expert of this.
I would create an animation of the interaction between D-Alanyl -D Alanine
carboxypeptidase and penicillin. In general i would see how the penicillin
attack the enzime that build bacterial's wall and I would see it in an
animation that it will processed into a Graphic 3D software (like as Maya or

I've a .pdb file of complex of the Streptomyces R61 DD-peptidase with
penicillin G (pdb ID "1pwc").
I would like to know if I can realize this trajectory with gromacs.
I would have initially two separate molecules in a solvent and and see how
these two molecules bind in an animation.

Some of you could give me directions on how to get this trajectory?
Thank you in advance.

View this message in context: http://gromacs.5086.x6.nabble.com/Protein-Ligand-simulation-tp5014482.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list