AMBER Archive (2008)

Subject: Re: AMBER: hold atoms fixed

From: Boutheina Kerkeni (b.kerkeni_at_ucl.ac.uk)
Date: Mon Jun 30 2008 - 08:12:33 CDT

Hi

my min_in file is:

  minimisation part1 + solvent + ions
  &cntrl
   imin = 1,
   maxcyc = 10000,
   ncyc = 5000,
   ntb = 1,
   ntr = 1,
   cut = 10
  /
Hold the part2 fixed
500.0
RES 797 9436
END
END

also in the min_out I checked it says:
    ----- READING GROUP 1; TITLE:
Hold the part2 fixed

      GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
  GRP 1 RES 797 TO 9436
       Number of atoms in this group = 8640
     ----- END OF GROUP READ -----

May be I should increase the force cst?
On 30 Jun 2008, at 14:02, Carlos Simmerling wrote:

> we need to see the rest of your mdin file to know why the constraints
> did not work- perhaps you didn't turn on that option?
> also look in the mdout file and make sure it reads this section and
> gives you some info saying it will use it.
>
> On Mon, Jun 30, 2008 at 8:51 AM, Boutheina Kerkeni
> <b.kerkeni_at_ucl.ac.uk> wrote:
>> Hi Amber users
>>
>> I have performed a minimization on a system composed of two parts
>> and my
>> point was to held fixed part2 by using the group utility/
>> Hold part2 fixed
>> 500.0
>> RES 797 9436
>> END
>> END
>>
>> But after minimization, when I visualised the correspondin pdb i
>> find that
>> all atoms in part2 has moved as well.
>> Is there a more specific way to freeze residues? atoms with Amber?
>> Thanks very much in advance for any help
>> Regards
>> Boutheina
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