AMBER Archive (2008)

Subject: Re: AMBER: question - gaff and leaprc.ff03ua

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Nov 23 2008 - 15:49:37 CST

On Sun, Nov 23, 2008, oguz gurbulak wrote:
>
> I want to ask if I can use leaprc.ff03ua force field directly in leap (
> not doing any operations like evaluating charges or generating a prepin or
> mol2 file ) for my n-alkanes simulations ?

No. The ff03_ua library only knows about proteins, not about general organic
molecules.

It's probably not hard to hand-build an n-alkane mol2 file, however. The
charges are likely to be all zero in a united atom n-alkane file, you you just
need coordinates and atom types.

[But/and: be sure you really want a united atom force field, especially going
forward to other systems (lipids?). There are some good reasons why very few
simulations use the united-atom approximation any more.]

....dac

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