[Chimera-users] Request for assistance

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 4 15:55:56 PDT 2013


Hi Zach,
Sorry, not off the top of my head. Potential sources of information:

- websites, documentation and user mailing lists or helpdesks for simulation packages, e.g. for AMBER:
http://ambermd.org/
http://ambermd.org/#reflector
http://ambermd.org/tutorials/
… and analogous for other programs

- journal article materials & methods sections, especially in respected journals from groups that specialize in computational chemistry (and are thus more likely to know what they're doing :-) )

-  general comp-chem discussion groups, e.g. could ask questions on CCL.net

Before you start sending emails or formulating pubmed queries, I recommend thinking more about what exactly you want to predict.  Do you want to predict change in stability, or in free energy of binding some ligand, or just what the protein might "look like" (probable conformations) with the mutation?  Is a precise quantitative result important?  It is best to ask as specific questions as possible, because if they are too broad or vague people are less likely to respond. If you don't  require quantitative results (e.g. free energy of folding decreased by N kcals/mol), less computationally intensive approaches may be the way to go… unfortunately either way will require a fair amount of legwork because of the vast number of possibilities. 

Brief searching turned up this review, and surely there are others
<http://www.ncbi.nlm.nih.gov/pubmed/20033914>

Another thing to consider seriously is seeking collaboration (or at least advice) from expert computational chemists, e.g. Friesner group at  Columbia.
Best,
Elaine

On Jun 4, 2013, at 1:35 PM, "Zachary W. Carpenter" <ZWC2101 at columbia.edu> wrote:

> Hey Elaine,
> Thanks for your quick response. Are you aware of any tutorials or wiki type instruction guides to getting started with more complex computational approaches to what I am describing? 
> Best, 
> Zach




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