AMBER Archive (2009)

Subject: Re: [AMBER] Improper dihedrals between residues?

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Jun 09 2009 - 16:17:03 CDT

> Hmm. So, if I understand you, you're saying that the improper specs in
> parm files are essentially ignored anyway?

No - the prep impropers are ignored, the parm ones are applied
wherever they can be.

> If that's so, I'll just use rdparm to see what's going on. And if I
> need to add an improper, it seems safest to follow Carlos' suggestion
> and use an NMR-type restraint.

I think this is better unless you need all of distance, angle, dihedral
-based forces to apply to your ion.

Bill

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