I have docked the protein and ligand by using autodock suite and have generated a docked complex, now i want to generate the molecular simulations of the docked complex by using gromacs 5.14. If we can generate what all steps do we need to follow to generate the simulations ?
yes, you can... just follow the tutorial of Gromacs for Protein-Ligand complex.
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
Oo thanks Anu Manhas, but i had a doubt that when i have gone through the tutorial i came to know that we need to submit both our Protein and Ligand compounds separately and even the generated results showed me the protein and ligand molecules were in the different boxes in different solvent system but not in a combined (Protein-Ligand) complex together in a single solvent system.
And does the gromacs 5.1 version support docking of the two different molecules and generate the simulations?
Hi Shashidhar, it seems that it's your first time to work on GROMACS. I am quite confused regarding the issue which you are facing. How did you manage to get two different solvents? If you are working according to the tutorial, then it's not possible.
You need to include the parameters for your ligand in the protein "topology" file. It is very clearly mentioned in the tutorial that to generate a single protein-ligand complex file, you need to merge ligand.gro file with protein's file and along with that you also need to manipulate your topology file by incorporating #include "drg.itp" (according to tutorial)
It is important that your topology and coordinate file should be in agreement with respect to the contents of the system.
Hope this will help.
Thanks Anu Manhas,ya as it is first time i was bit confused but later on everything got cleared and i have succesfully completed molecular dynamics simulations of the protein-ligand complex.
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