Using Discover and FF converted by AmberFFC, NEUTRAL termini amino acids are not recognized. WHY ?
Here are typical errors: (Executing: Potentials Forcefield Fix -Print_Potentials Fix -Print_Part_Chargs Fix -Print_Form_Chargs TEST) Using template file ‘/usr/people/guest/AmberFFC-1/empty_templates.dat’ for potential assignment for residue TEST:1 Could not assign potential type to TEST:1:N Could not assign potential type to TEST:1:HN1 Could not assign potential type to TEST:1:HN2 Could not assign potential type to TEST:1:CA Could not assign potential type to TEST:1:HA Could not assign potential type to TEST:1:C Could not assign potential type to TEST:1:O Could not assign potential type to TEST:1:CB Could not assign potential type to TEST:1:HB1 Could not assign potential type to TEST:1:HB2 Could not assign potential type to TEST:1:HB3 Warning: total formal charge does not equal total partial charge. ANSWER With InsightII, you can select which termini you want for your peptide/protein: – Either neutral (NH2) or charged (NH2+) amino group – Either neutral (CO2H) or charged (CO2-) acid gr
