Re: AMBER: prepin file format description; pointers on parameterization

From: David Mobley <>
Date: Wed, 24 Oct 2007 13:45:54 -0700


> > I don't care what file format I use. I'm just trying to figure out how
> > to use the files that are provided with the distribution (which are in
> > prepin format), i.e., first I need to know how to interpret them
> > myself so that I can edit them. Alternatively, if there's a tool I can
> > use to convert them to some other format that would be easier for me
> > to edit myself, that's great. All I need is (a) the files in some
> > format I can understand and edit, and (b) to be able to read it into
> > leap to describe the residue.
> Instead of editing, you could also use LEaP scripts to add the
> information required to construct a FF library.
> You could study the LEaP script for 10 solvent (whole) _molecules_ at:
> You could study also this other one for 32 DNA/RNA _fragments_:

OK, this is becoming more clear now. Thanks!

I think you might want to be careful in defining terms; it appears to
me you're using the term "FF library" to mean "any file which
specifies atom type and connectivity information", and this isn't the
only possible meaning.

> > I guess as you're suggesting perhaps I can just read it into leap and
> > save it as a mol2.
> Yes, for instance.
> However, in your case because I guess you will have to handle
> molecular fragments the best bet might be to use the OFF format since
> it can contains information about connecting atoms between fragments.
> Or you could use mol2 files as FF precursors for OFF FF libraries. It
> is the strategy used in R.E.D./R.E.DD.B. ;-)

Again, I don't care about what file format I use. All I care about is
getting the parameters right and ending up with a prmtop I can use.

> prepin, mol2, OFF and RTF (CHARMM) are only FF libraries. More or less
> the same. Please, read the Tripos mol2 description in the
> tutorials: you will find information about FF
> libraries...

This is where I got confused about what you meant by "FF libraries",
but then I figured it out (see above).

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Received on Sun Oct 28 2007 - 06:07:14 PDT
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