Re: [AMBER] parameters from frcmod not overwriting gaff.dat

From: David A Case <>
Date: Thu, 9 Jan 2014 07:56:21 -0500

On Tue, Jan 07, 2014, Allen, Scott Edward wrote:
> My frcmod has explicit parameters for the X-cd-c -X dihedral (as in,
> I explicitly define all 4 dihedrals about this bond), but when I run
> rdparm --> printDihedrals on the resulting prmtop file, I see my
> parameters AND the parameters from gaff.dat defining all the X-cd-c -X
> dihedrals. I can work around this by deleting all gaff.dat-originating
> dihedrals manually in rdparm, or by using my own gaff.dat with the
> X-cd-c -X dihedrals deleted, but aren't the dihedrals from frcmod
> supposed to overwrite the ones from gaff.dat?

I can think of reasons, based on the way wild-card parameters are stored
interally, why frcmod files might not correctly replace wild-card parameters.
Sounds like at a minimum we need to document this behavior.

Generally, Amber developers tend to thing of wild cards as "evil", since it
can be hard to predict and control their behavior. But we've never taken the
full plunge to eliminate them entirely.


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Received on Thu Jan 09 2014 - 05:00:03 PST
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