Hi Per,
Thanks for your quick reply. Hopefully it will work.
Best Regards,
Ioannis
________________________________________
From: Per Jr. Greisen [pgreisen.gmail.com]
Sent: 23 March 2011 20:14
To: AMBER Mailing List
Subject: Re: [AMBER] how to minimize a protein-ligand system with the protein constrained
Hi
Keep ntr=1 and then add the following lines to your md-input file
/
Hold protein fixed
500.0
RES 1 100
END
END
RES is the number of residues in your protein - here is given an
example of 100. 500 is the weight and that should keep your protein
fixed.
With kind regards,
On Wed, Mar 23, 2011 at 9:09 PM, I.Haldoupis <ih2g09.soton.ac.uk> wrote:
> 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,
> Ioannis.
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Per
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Received on Wed Mar 23 2011 - 15:00:02 PDT
