Re: [AMBER] Multiple Harmonic Restraints

From: Thomas Gaillard <>
Date: Tue, 23 Feb 2021 18:20:41 +0100

Le Tuesday 23 February 2021 à 04:44:27PM, Li,Haoxi a écrit :
> Dear Amber Users,
> I was trying to apply different harmonic restraints on different residues by using GROUP specification at the end of the input file, but it was not very clear to me on how to select non-hydrogen heavy atoms with the filters. Is there an easy way to do this with GROUP specification? Or instead, can I use different amber masks (like restraintmask=':1-30,90-100&!.H=‘, ‘:120-130&!.H=‘ restraint_wt=5.0, 10.0) for different restraints values? Thank you!
> Best wishes,
> Haoxi

Dear Haoxi,

If needed, you can edit the TREE_CHAIN_CLASSIFICATION parameter of the
prmtop with Parmed to define arbitrary selections for the GROUP syntax.
See the following messages:


Thomas Gaillard
Professeur assistant
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
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Received on Tue Feb 23 2021 - 09:30:02 PST
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