Sunday, February 6, 2011

Course: QM/MM modeling of enzymatic reactions

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).


Vladimir Chupakhin said...

Very interesting!

Anonymous said...

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

Jan said...

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.

Anonymous said...

I prof Jensen, I'm I big fun of your BLOG. I'm performing an ONIOM analysis on a Enzyme. Starting from the omptimized geometries I need to make a MD (with NAMD). So I need to generate from my out a PDB and after a PSF files. The problem is that in the generation of the PDB some atoms are not recognized and so the PDB results to be well written.
I tried to do taht with Avogadro, VegaZZ and a package calls TAOPACKAGE but the problem is the same: the information concerning the extra atoms (i.e substrate) that are not present in the primitive PDB are not recognized.

Can you help my suggesting a method to generate a PDB from the ONIOM gaussian out?

Best regards

Paolo Piazzetta

Jan Jensen said...

I am afraid I don't have much experience with Gaussian. Try asking on the mailing list.

Anonymous said...

Thanks for the answer. The problems is not linked to gaussian.out but more generally to the generation of PBD file from QM/MM log or out obtained with Gamess,NWchem,g09....

When you perform a MD do you use only PDBs from protein data bank or you make Molecular Dynamics calculation on your optimized sistems?