I have been working on understanding the mechanism of efflux mediated drug resistance in bacteria. I was able to successfully model the protein using homology modelling and threading. Now I would like to dock the antibiotic and run molecular simulations. However, I am not sure of the parameters (steps in energy minimization, type of AMBER force field to be used, methods to run MD simulations, total time to run the simulation and calculating binding free energies). As I am new to this field, I request you to kindly provide me any guidelines or other references where selection of these parameters is mentioned. Thank you.
For the MD simulation study, You can use GROMACS software which is open source software. You want to study the efflux behavior of protein, so u can use the given below link.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/
If u will get some specific problem, u can let me know. Definitely I will help you, specially in the SMD (means during effulx study).
Regards,
Nandan
Gromacs is an open source platform where you can simulate your desired protein easily. The Details of parameter setup guide is given in link as an example
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
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if you can't understand from here, just go to official site of gromacs. user mannual and itger documentation are there
If you want to use Amber force field for you ligands, you can perform a tandem of gaussian, Ambertools and acpype software calculations.
After getting your model, insert protein in lipid by using CHARRM-GUI server. Collect the gromacs formated topologies from there. As you want to do docking and want to see the binding energy then do simple protein lig simulation. There are so many articles available. You can also follow my recent papers on ABC transporter protein simulation.
I am surprised that none suggested NAMD along with Gromacs to run MD simulation. You can use CHARMM36 force field in NAMD to run your MD simulation which has excellent force field parameters to use.
A preliminary model of the antibiotic can be prepared in a couple of minutes with the PDC in the DREIDING force field in the Abalone program. This model can be tested in a graphical environment. If it looks promising, then it can be incrementally improved and eventually transferred to the usual simulators on the cluster.
http://www.biomolecular-modeling.com/Abalone/Simulations.html
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