I am trying to to create a non-standard residue - HCN. This cannot be done by the Dundee PRODRG server as it subsumes the polar hydrogen into the carbon. This results in a diatomic molecule that the program cannot handle.
I do mind creating a new drug by hand, but a search through the email list has been less than fruitful. I have done parameter/non-standard residue formation in AMBER, I believe I understand the process. Yet, there is no clear delineation of how one does charges. The best I found was the proper suggestion that CHELPG charges from a QM calculation should be employed. This is to be expected, but WHICH method should one use: hf/6-31g*, MNDO, something else? I know I will have to augment my parameter file to include the new atom types and parameters. But as HCN has a polar hydrogen "on a carbon" how do I ensure that this is explicitly maintained? If I lie and call the hydrogen on carbon "H", the designation for an atom bonded to Nitrogen, is this enough to keep that hydrogen explicit? I also want to make a solvent box of HCN (cheaper and safer than trying this experimentally!!). I am assuming that simple electrostatics balanced against Van der Waals interactions will dictate the proximity of hydrogen bond donor to acceptor in this forcefield. Finally, I assume a kluge of non-bonded parameters (van derWaals) is reasonable or is there a preferred way of determining an L-J potential? If I totally missed the answers to these questions, a hint on better keywords or a good reference encompassing these issues would be welcome. Thanks. Mark
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