From parisien@iro.umontreal.ca Wed May 11 23:16:48 2005 Date: Tue, 19 Apr 2005 08:54:46 -0400 (EDT) From: Marc Parisien To: Bruno Contreras Moreira Cc: xiangjun@rutchem.rutgers.edu Subject: Re: help with DNA deformation energy Hi Dr. Bruno, > I've just found your deformation energy code at > http://rutchem.rutgers.edu/~xiangjun/3DNA Cool! > What's the energy reported? is it the energy that you need to apply to the > system to obtain a given DNA deformation with a given sequence? It is a deformation energy (units are kcal/mol, I think) based on population preferences: E = -RT ln( P ) where P is the probability of finding the sample in that conformation. This deformation energy reaches back to Go where he analyzed the protein helix deformations (I don't have that reference). I suggest that you imperatively read the 2 articles mentionned in the "credits" section of the program (in the main() routine). > Do you need full-detail PDB coordinates of the DNA or the backbone is enough? > Thanks for your feedback and for the code!! Unfortunately, you need the full DNA since the energies come from the side-chain conformations. You will have to launch the 3DNA program before calculating the energies. The energies reported here are not to be confused with those reported by force-fields like AMBER or CHARMM... the energies here are those only from population samples! You would have to do a thermodynamic cycle to obtain the energy to apply to the system to obtain a given DNA deformation with a given sequence! As an application of this program you can look at a DNA/Protein complex and do in-silico DNA mutations by changing the nature of the nucleotides but without modifying the DNA 3D structure... You can then select the best DNA sequence for that particular DNA 3D structure... Do not mix the 2 energies calculations: use my program with the "-s" option (the step energy) or with "-b" (the base-pairs energy)... Regards, Marc. //-------------------------------------------- Marc Parisien parisien@iro.umontreal.ca www-lbit.iro.umontreal.ca