Hi, all.
I don't think we have a good "default" water model yet: TIP3P is indeed
widely used, but its bulk properties deviate most from experiment, see
e.g. a recent review by Vega and Abscal,
http://www.ncbi.nlm.nih.gov/pubmed/21927736
best, Alexey
On Sun, Mar 8, 2015 at 9:31 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> 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 Mon Mar 09 2015 - 18:00:03 PDT
