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From: Jose M. G. <jos...@un...> - 2015-08-26 14:56:35
|
Dear rDock community, After docking molecules containing NH2 attached to aromatic ring (sp2 nitrogen), the two hydrogens are not in the same plane as the N-ring. I believe this issue came from the force field. I therefore analysed the force field used in rdock and noticed that several force fields are actually mentioned (in $RBT_HOME folder): - masses.rtf : Insight97and Charmm27 - in folder sf, files Tripos52 (dihedral.prm, vdw.prm, vdw.prm.old) I think Tripos52 is applied to the receptor (correct me if I'm mistaken), but what for the ligand? How are used the parameters extracted from Charmm27 and Insight? Secondly, I would like to know if it's possible to modify/use another force field instead of the one implemented in rDock for ligands? Thank you for your help! Jose Manuel |