[Chimera-users] energy optimization of the modle from homology modeling

Tom Goddard goddard at sonic.net
Mon May 13 11:38:34 PDT 2013

How to make a suitable homology model for docking and what force fields to use are not questions specific to Chimera, they are questions about how to do good quality science, and they depend a great deal on the details of your system. So you aren't likely to get the answers you want on this list.

I'm not at all an expert on docking or homology modeling.  Docking to a homology model may be a fruitless effort no matter how you do it.  That said, energy minimization will just get your homology model to a nearby local minimum, while MD could make larger changes.  Both might be worse than the unmodified homology model if it is based on a very similar structure to your target.

I don't know what force field is good for NAD+ bound to a protein. 

If you want only conjugate gradient steps and no steepest descent steps then set steepest descent steps to 0.  But the steepest descent steps are much faster and could help you get to a minimum faster than with conjugate gradient alone.  How many steps are needed depends on your system.  By trying different numbers and seeing how much change is made you could find out how many are needed.


On May 11, 2013, at 6:50 PM, aixintiankong wrote:

>   Dear,
>    i am a newer use the chimea, i have some question to consult to you, please help me.
>   Frist, after Homology modeling using the chimera modeller, should i optimizate the modle by energy optimization or Molecular dynamic simulations? The next step i will use the model to make docking.
>   Second, i want to use chimera to minimize the structrue of my modle.   i select Tools>Structure Editing>Minimize Structure to perform my work, but my modle include protein and a organic molecule NAD+, so i don't know how to select the force fileds for the minimiztion of the modle. please help me.
>   Third, if i olny want to use the conjugate gradient to perform the minimiztion, should i only need to set the steepest descent steps to 0?  in general, how many conjugate gradient s! teps and size should be ?
>   Thank you very much!
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