Hi Gmx Users, I am building a surface as a reperesentation of protein surface. In this case I divide amino acids as: polar, nonpolar, positively charged and negatively charged. Representation of 3 atoms constitutes one residue. I created new residues (Charmm27) using exsiting charges:
e.g. Residue - Negative [ NEG ] [ NEG ] [ atoms ] CC C 0.34 0 OT1 OC -0.67 1 OT2 OC -0.67 2 [ bonds ] CC OT1 CC OT2 Theses charges are taken from COO- group of terminal residue [ GLY ]. I am able to find partial charges for Hydrophobic (CH2). However, I cannot find for positive representation of 3 atoms) for positive or hydrophilic residues. They always come as 2 or 4 atoms giving positive (+1) of neutral (hydrophilic). My question: Can I create me own partial charges for given positive or hydrophilic group? Is that ok for the force field? As different atoms in different groups have different charges it should be fine in this case... I will appreciate your response. Thank you! Steven
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