If anyone have gromacs tutorial to a new residue to the topology. The protein which I am working on has 4 NAG (N-acetyl Glucosamine) and 1 ALS (2-amino 3-oxopropionic acid). These residues were not found by Gromacs because these molecules are not present in the residue topology database.
I need a tutorial to modify these database files and run the simulation with these molecules.
Thanks
Please visit this website and you will find the way;
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
Dear Pankaj Mishra,
I have already gone through that website. And I am looking for tutorial where I can learn and perform the simulation of my protein of interest.
Here, download .itp file for 1 ALS (2-amino 3-oxopropionic acid)
http://compbio.chemistry.uq.edu.au/atb/molecule.py?molid=4770#panel-md
Accrodingly, you can do for NAG.
Also, you will not find any tutorial specifically for this but if you want a general tutorial for MD simulation, you can visit these site;
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html
http://compbio.biosci.uq.edu.au/education/mdcourse/Lysozyme.html
You can also see this,
http://comments.gmane.org/gmane.science.biology.gromacs.user/48856
if you any problem let me know
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