AMBER Archive (2009)

Subject: Re: [AMBER] query

From: Pansy Patel (
Date: Fri Jul 31 2009 - 09:41:05 CDT

Hello Bharat

You can use restraining it like so:

  ntr=1,restraint_wt=4.0,(you can change the weight)
  restraintmask=':residue number', (it can be a list of residues as well in your alpha helix)


>>> bharat lakhani <> 07/31/09 3:43 AM >>>
Sir / Madam,

During minimization if i want to fix the secondary structure part
(alpha helix) and move rest of the part is it possible to do it ?
I mean a type of constrained minimization where internal
parameters(bond angle,bond length,backbone torsion angle) of helix is
fixed its behaving as one big molecule. So it is moving as one
molecule from one place to another without disturbing the helix

Can you please tell me the process to carry these things.


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