[gmx-users] Protein - Ligand simulation

Aldo Segura asegurac666 at yahoo.com.mx
Tue Feb 11 20:48:32 CET 2014

You should take a look at this tutorial:




Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cancer and Blood Diseases Institute
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera at cchmc.org; aldosegura at gmail.com

El Martes, 11 de febrero, 2014 14:25:36, lucaam86 <borroluca at gmail.com> escribió:
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.

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