[AMBER] how to minimize a protein-ligand system with the protein constrained

From: I.Haldoupis <ih2g09.soton.ac.uk>
Date: Wed, 23 Mar 2011 20:09:13 +0000

Dear Amber users,

I am a new user and I need to initially perform a minimization of my
protein-ligand system keeping the protein rigid.

I have seen in the tutorials and the manual that there are different
ways one can restrain atoms: the command ntr with restraint_wt and
restraintmask; ibelly with bellymask ( I will be performing that in GB
solvent i.e. igb>0 so I am not sure if this option is available); Belly
Group; Group Input (as in tutorialB1: Simulating a small fragment of DNA
section 5.1.3.

However, is there a method that can keep the protein completely frozen?
Would placing a very high restraint weight achieve that?

Has anyone faced a similar issue?

Best wishes,

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Received on Wed Mar 23 2011 - 13:30:02 PDT
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