Dear Justin, Thank you very much for your response. I have another question to continue my calculations.
To correct charges and charge groups I have to: 1) seprate the molecule to functional groups 2) some of these functional groups are already exist in selected force field ( in aminoacid.rtp) with their charges, so as you said in fifth tutorial "life is pretty easy" 3) for new functional groups I have to: i) do QM calculation ii) calculate free energy of solvation or logP iii) compare simulation results with experimental data my questions are when my simulation results do not have any consistence with experimental data, how can I modify new functional groups? and how can I decide which one of atoms have improper charge? Thanks a lot in advance. P.Haghighi
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