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-- Yong Duan, Ph.D, Professor UC Davis Genome Center and Department of Biomedical Engineering University of California at Davis Davis, CA 95616 530-754-7632 On 12/11/11 3:03 PM, "B. Lachele Foley" <lfoley.uga.edu> wrote: >I would still argue for a list because it will help people who are trying >to decide which force fields can be used together. Since the Leap's >don't complain if something is multiply defined, it becomes easy for >parameters to silently be mis-loaded. And, while you can say "the user >needs to learn to go look in the files," it seems we could make that a >little easier. For example, if one merely looks at the defs at the top >of parm94.dat, you would think CY isn't being used. And, it isn't -- >except for a van der Waals-type equivalence near the bottom. > >Perhaps CY wasn't a great choice, but it seemed as if parm91 was merely >claiming it for some future use (as carbon-13, apparently), and its use >had been mostly dropped by 94. In 94, its remaining as a vdW equivalent >was probably just an oversight. So, it wasn't being used anymore, as far >as we knew. > >What I'm saying is that if an atom type is used in something so old it's >been hidden down in "oldff", should we still worry about reusing it? In >04, the CY type hadn't been written significantly into a "parm" force >field in 13 years. Maybe we shouldn't ever reuse, but there are only so >many 2-letter combinations. > >We can't just load glycam as a frcmod afterwards. The trouble is that >the definitions are too different. Our CY is sp3, and others are sp2. >So, we have to load our atom types, then their atom types, then their >parameters, then our parameters. > >:-) Lachele > >Dr. B. Lachele Foley >Complex Carbohydrate Research Center >The University of Georgia >Athens, GA USA >lfoley.uga.edu >http://glycam.ccrc.uga.edu > _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Sun Dec 11 2011 - 15:30:03 PST