[gmx-users] Protein - Ligand simulation

Justin Lemkul jalemkul at vt.edu
Wed Feb 12 02:58:35 CET 2014

On 2/11/14, 2:48 PM, Aldo Segura wrote:
> You should take a look at this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html

It's worth noting that while what the OP is trying to can be accomplished using 
SMD, the time investment would be quite significant.  Proper implementation of 
the pull code, coupled with selective restraints on the protein (hitting a 
moving target!), and parametrization of penicillin to be at least reasonably 
stable during the simulation all present challenges, especially for a 


> Best,
> Aldo
> =======================================
> 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
> Blender).
> 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.


Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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