[gmx-users] All-atom vs United-atom force fields and hydrogen bonds

[Jason Hill]

Hello list,

I’m working with some allozymes that differ by only a couple of amino acids but that I have observed to have empirically very different binding affinities and thermal stabilities. I’m investigating the structural basis of the functional differences so I crystallized one form and am using that structure as the template for a molecular dynamic approach. Among results that I am interested in are hydrogen bonding patterns. I’ve been reading the primary literature for the force fields and I’m sorry to say I am still unclear on what I think are a couple of basic issues, ones that I hope you can help me figure out.

1) When a united-atom force field is used suck as GROMOS96 54a7 are the hydrogens of ALL carbons in the system subsumed into the carbon and if so are their position on the carbon kept track of?

2) When selecting a force field is information lost in a united-atom force field like GROMOS96 54a7 that renders downstream analysis by tools like g_hbond less meaningful?

3) One of my favorite up to date tutorials (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/index.html>) uses the OPLS-AA/L force field but a lot of the literature seems to indicate that the newer force fields perform much better (blog review: http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields <http://md.chem.rug.nl/cgmartini/index.php/blog/265-comparingforcefields>)! Is the all atom parameterization so much more important than factors like agreement with NMR structure for down stream analysis for g_hbond or other things that OPLS-AA/L would still be a better choice?

4) For a protein in water simulation in which you were investigating the movement and stability of the protein, what force field would you use, and why?

Thanks in advance for giving this a thought, and happy new year!

Best regards,
Jason

Jason Hill, Ph.D.
Wheat Lab
Zoologiska Institutionen
Stockholms Universitet
D-419 Svante Arrhenius v 18B
S-10691 Stockholm Sweden




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