I have a protein with ATP inteacting with a "medium" ligand and I like to study the hydrogen bonds between the ATP and the ligand, and see if there are any pi-pi stacking as well in other part of the ligand.
Pi-pi interactions are governed by electron correlation effects. I've never heard of a potential that actually write it down explicitly in the force-field expression. I did read about regular LJ potential is able to capture some of the energtics of pi-pi though [http://www.ncbi.nlm.nih.gov/pubmed/16425171], in this case it is the AMBER forcefields.
If you really wish to study those interactions in fine detail maybe you should do a QM/MM study in your particular system of rings. And the more correlated your wavefunction is, the better a description you will have. If accuracy is not your worry but you'd rather just have a somewhat rough description of the event, then the information you want is probably in the LJ energy profile of your system accross the trajectory.
Pi-pi interactions are governed by electron correlation effects. I've never heard of a potential that actually write it down explicitly in the force-field expression. I did read about regular LJ potential is able to capture some of the energtics of pi-pi though [http://www.ncbi.nlm.nih.gov/pubmed/16425171], in this case it is the AMBER forcefields.
If you really wish to study those interactions in fine detail maybe you should do a QM/MM study in your particular system of rings. And the more correlated your wavefunction is, the better a description you will have. If accuracy is not your worry but you'd rather just have a somewhat rough description of the event, then the information you want is probably in the LJ energy profile of your system accross the trajectory.
No. Simple programs are MOE, Abalone, Sybyl, perhaps Tinker.
If you do not have a ready force field for ligands and want to use some automatic approximation then MOE or Abalone.
Force fields are portable between programs. All of these programs use near the same force fields sets. The difference in the programs are speed and convenience, but not accuracy.
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