Aha, I see now what's going on. The prmtop I'm dealing with was given to
me by someone else and it must have been made with a parmchk2-derived
frcmod file. Problem solved.
Cheers,
Dave
On Mon, Mar 28, 2016 at 9:13 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Mar 28, 2016, Dave Cerutti wrote:
> >
> > I've come to realize that, in GAFF, Junmei is playing a very
> sophisticated
> > game. The parameters listed in gaff.dat aren't precisely what appears in
> > the resulting prmtops. There are, instead, a rich set of rules listed
> > elsewhere on our website by which those parameter prototypes get
> > post-translational modifications to make a functioning system. In light
> of
> > this, I'm trying to figure out how one can go about parameterizing a
> ligand
> > with mostly GAFF yet introduce some specific modifications of his own
> (the
> > new modifications would not be meant to go through the mixing and
> > modification that other GAFF parameters do).
> >
> > Looking at the sustiva ligand parameterization tutorial and the general
> > strategy with paramfit, it seems the things to do is write a frcmod file
> > that then gets read in to supplement or overwrite the original
> parameters.
> >
> > So... is the answer that GAFF can be modified with a frcmod file, and
> tleap
> > knows to apply various mixing rules and contexts to modify GAFF's
> prototype
> > parameters, but if it then sees a frcmod file with relevant parameters it
> > will apply those at face value, overwriting the GAFF-generated numbers?
>
> I'm not sure I understand your question. The parmchk2 program uses the
> rules
> you mention above to create a frcmod file specific to the molecule it is
> dealing with. tleap knows nothing about "prototype parameters" or
> "mixing rules and contexts". All tleap sees are these two statements:
>
> source leaprc.gaff <-- reads in general parameters
> loadAmberParams frcmod.<yourmolecule> <-- file created by parmchk2
>
> tleap doesn't have any idea where the parameters came from, or whether they
> are GAFF parameters or not: all those "smarts" are in parmchk2.
>
> So, just load yet another frcmod file (after the two above) if you want
> to make further modifications to the parameters that actually get into the
> prmtop file. All parameters read into tleap are treated at "face value".
> Later frcmod's over-write earlier ones.
>
> Hope this helps...apologies if I have misunderstood your question and are
> just
> telling you things you already know....
>
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 28 2016 - 20:00:02 PDT
