AMBER Archive (2009)

Subject: Re: [AMBER] Specifying improper dihedrals

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Jun 17 2009 - 14:25:55 CDT


> I wasn't talking about parm.dat or frcmod files, but rather the final prmtop.

I know, but I was thinking the same '3rd atom ist the central one'
convention likely appears in prmtop too: hmm, maybe it doesn't matter
once the match is made.

> As it happened, the improper dihedrals I added I couldn't
> specify there anyway; they're the ones I emailed the list about the
> other day which span residue boundaries in unconventional ways.

The impropers from parm.dat/frcmod should be easily applied at residue
boundaries - the problem with residue boundaries is just in the unused
legacy prep.in format.

Bill

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