I have an enzyme, which has a small one turn alpha helix present on a loop surrounding the active site. I have to mutate one of the residues on the alpha helix with proline, so that it may be a part of the extended loop. How can I perform Gromacs simulation for this? Can I visualize this helix to coil transition through a movie?
Hi,
You can simulate this like normal, you'll just need to generate a new topology file. When you do your analysis, analyze the secondary structure with gmx do_dssp, using the -ssdump flag.
As for making a movie. I'm not sure how other programs do it, but in VMD, the secondary structure type is based on what VMD determines in the first frame, Therefore, in order to make a movie of this transition, you would need to load and render each frame individually, and then find a program to combine them into something else (mp4, gif, etc)
Cheers,
John
John H Dupuis
Thank you very much Mr. Dupuis for your suggestion. I installed the dssp program and trying to use gmx do_dssp.
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