I am teaching a graduate course QM/MM modeling of enzymatic reactions. Though this is about as non-basic as you can get in molecular modeling it may be of interest to some readers of this blog.
In addition to the course website, which includes a list of papers and lectures slides updated weekly, I also hope to make blog posts summarizing the in-class discussion. This will happen over at Proteins and Wave Functions, a new group blog I have started to facilitate group communication - both within the group and with the scientific community at large (constructive comments from anyone are greatly appreciated).
Posts
3 comments:
Very interesting!
Hi,first I want to tell you that your blog is very useful, really!
I hope that you cant help me: I'm working on an optimization of a peptide structure, in the alfa-helix conformation.
After I need to know the energy of the peptide having a bent structure. Now, I don't know in which way I can bend the structure manually, because when aI try to do that (with Avogadro for example),
I loose the alfa helix conformation. I tried to import in Avogadro the structure builded whit MarvinSketch but the starting geometry is unreal, and this compromise the optimization process.
There is a easy way to bend the structure with Avogadro?
p.s I'm using Hyperchem to optimize because there is AMBER inside; usually i use GAMESS.
Thanks a lot
I'm not sure there is a general answer to your question, rather I suspect it's a matter of trial and error.
In Avogadro, starting with and alpha helix, I would try to constrain an angle between atoms at the too, middle, and bottom to some relatively small value, optimize, and then gradually decrease the angle.
Another option is to search the PDB for structures with bent alpha helixes, and extract them.
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