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Hi all, I am using ccpn/aria/cns combination for my structural work. I discovered a probably bad fact during the aria/cns structure calculation. In the ccpn project, His side chains are defined to be protonated at both sidechain nitrogens (ND1-HD1 & NE2-HE2) by default. This might be a correct description during assignment especially for exchangeable solvent exposed histidines, but in cns it results in the fact, that the sidechain is positively charged by default. This is from the psf file: loop_ _cns_mtf_atom.id _cns_mtf_atom.segment_id _cns_mtf_atom.residue_id _cns_mtf_atom.residue_name _cns_mtf_atom.atom_name _cns_mtf_atom.chemical_type _cns_mtf_atom.charge _cns_mtf_atom.atom_mass ... 113 ' A' '5' 'HIS' 'CG' 'C5' 0.330000 12.0110 114 ' A' '5' 'HIS' 'ND1' 'NH1' -0.540000 14.0070 115 ' A' '5' 'HIS' 'HD1' 'H' 0.460000 1.00800 116 ' A' '5' 'HIS' 'CD2' 'CR1H' 0.330000 12.0110 117 ' A' '5' 'HIS' 'HD2' 'HA' 0.00000 1.00800 118 ' A' '5' 'HIS' 'CE1' 'CRHH' 0.500000 12.0110 119 ' A' '5' 'HIS' 'HE1' 'HA' 0.00000 1.00800 120 ' A' '5' 'HIS' 'NE2' 'NH1' -0.540000 14.0070 121 ' A' '5' 'HIS' 'HE2' 'H' 0.460000 1.00800 This results in an netcharge of +1 for the sidechain. Shouldn't it be more precisely defined depending on the actual pH the measurement was done in? Many NMR structures are determined around the pKa of the histidine side chain at which we have an equilibrium between 0 and +1 charge resulting in only a slight positiv charge. I am not a forcefield specialist, but I would assume this difference might make an impact on calculating the electrostatic interactions? And if we assume a higher pH it becomes very unlikely to have a charge. I don't know which model will be the best, keeping the double protonation, but adopt the charge or adopt the occupancy of the protons and with that also lower the charge. Or whether the impact is too small for all this. Thanks, justin P.s. Sorry for the cross-posting, I weren't sure, whether we should export from ccpn to aria more fine tuned, whether Aria should take care of this during the creation of the template molecules, or whether this is a problem of cns and NMR. -- Justin Lecher Institute of Complex Systems ICS-6 Structural Biochemistry Research Centre Juelich 52425 Juelich, Germany phone: +49 2461 61 2117