Sometimes new systems will have a non-standard residue that needs to be parameterized in order to run molecular dynamics. What does that mean? Well, it means your research project is so special that nobody’s every needed (or if they did, they didn’t make it public) the set of parameters for something in your system. That said, a few hours scouring the internet could save you the pain and suffering (fine, maybe just the time and mild annoyance) of having to generate parameters for non-standard residues. Two good places to check are the RESP ESP charge DData Base Home Page (they were trying real hard to stay with a theme…) and the University of Manchester AMBER parameter data base.
If you’re not lucky enough to have pre-generated parameters, then you get the
pure and utter joy of either using antechamber in AMBER yourself
(which isn’t all that bad for small organic compounds) or uploading some
information to
PyRED program interfaced by RED Server Development.
PyRED is an interactive submission process that a mol2 (charge file) and
the wanted frcmod (parameter file).
You can then convert the mol2 to a prepi file using antechamber if you
would like.
PyRED has a
tutorial
available on how to generate certain types of non-standard residues.