----- Original Message ----- From: Mark Zottola <[email protected]> Date: Friday, June 4, 2010 1:55 Subject: [gmx-users] Creation of a Non-Standard Residue To: Discussion list for GROMACS users <[email protected]>
> 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? The standard advice is here http://www.gromacs.org/Documentation/How-tos/Parameterization. For starters, choose a force field you want to parameterize HCN to work *with*. > 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. > You seem to be creating problems for yourself by not having a clear objective - or at least not expressing it here! > 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? Guessing values randomly is likely to get random results. Parameterization and validation of parameters are difficult topics to work on, and not encouraged for newcomers. > If I totally missed the answers to these questions, a hint on better > keywords or a good reference encompassing these issues would be welcome. Mark
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
