Normally we use AMBER and CHARMM for protein minimization. Can anyone tell me which one is better AMBER or CHARMM?
Here you can find a list of references which compare different force fields used in md simulations of biomolecular systems
http://www.ncbi.nlm.nih.gov/m/pubmed/18446282/
Price and Brooks, j. Comp. Chem, 23, 1045, 2002.
You can also see the references therein.
Here you can find a list of references which compare different force fields used in md simulations of biomolecular systems
http://www.ncbi.nlm.nih.gov/m/pubmed/18446282/
Price and Brooks, j. Comp. Chem, 23, 1045, 2002.
You can also see the references therein.
Consistent Force Field (CFF) does it all (protein, small ligands, RNA, DNA). It is available with Discovery Studio, by Accelrys.
At a conference I was at last week, an expert suggested that you should try at least two, and preferably three, force-fields. If you get the same result, then you have good confidence that everything is working well. If your result depends on the force-field, then you would have to be suspicious.
Since we don't _really_ know what the correct terms for the van der Waals potential are (and this is pretty fundamental to protein folding), all of the force-fields necessarily involve a degree of approximation.
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