We have not yet addressed the problem of force field naming that was brought
up at the Amber developers' meeting in February. Some notes:
1. Section 3.2.1 of the manual still reads as though ff14SB is only for
proteins. There is one tiny sentence, many paragraphs later, that indicates
it could also be used for RNA; nothing about whether it might be good for a
combination of proteins and nucleic acids.
2. Table 3.1 is not as helpful to users as it should be. It lists of bunch
of modifications, but gives no indication of *how* to load any of the force
fields that are listed there.
3. We talked about having separate leaprc files for proteins, DNA and RNA,
but Jason has noted potential problems with this. I don't have a suggested
solution (and I've not really heard one): but we need very soon to come to
some agreement, and to have appropriate leaprc files for various recommended
combintations of parameters.
4. On a related topic: we need a better way for a user to specify water and
ion parameters. Specifying TIP3P water should automatically load the
associated ion paramters; same for other supported water models. This should
probably be implemented by having a leaprc.tip3p that performs these actions.
5. (I can do this one): the beginning of section 3.1 should probably suggest
to people that they load a "leap.in" file, which in turn would load *several*
leaprc files for the components they need. That is, the "standard" would be
to expect to load at least a protein and a water/ion file; if there are
ligands, one would usually load leaprc.gaff; if one has lipids
or nucleic acids or carbohydrates, one would load additional files.
Suggestions are both welcome and needed....thx...dac
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Received on Sun Mar 08 2015 - 07:00:03 PDT
