AMBER Archive (2009)

Subject: Re: [AMBER] query

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Fri Jul 31 2009 - 20:23:07 CDT

Hello everyone, Pancy is right about it. You can use the following
script changing your residues number or location in the constraint
residue option.

&cntrl
imin=1,
maxcyc=100,
ncyc=50,
ntpr=10,
ntb=1,
ntx=1,
ntr=1,
ntf=1,
cut=10,
scee=1.2,
scnb=2,
nsnb=25,
dx0=0.5,
drms=0.000001,
ntxo=1,
&end
Group input for restrained atoms
25
RES 1 138
END
END

Regards
Ashish Runthala

On Fri, Jul 31, 2009 at 8:11 PM, Pansy Patel<pdpatel_at_mail.ucf.edu> wrote:
> 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)
>
> Pansy
>
>>>> bharat lakhani <lakhbharat_at_gmail.com> 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
> structure.
>
> Can you please tell me the process to carry these things.
>
> Thanks
> Bharat
>
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-- 
Ashish Runthala,
Faculty Division III,
Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031
INDIA

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