In the previous reply, in 2) I said "by making r2 equal to r2", it should
be corrected as "by making r2 equal to r3"
On Wed, Apr 2, 2014 at 9:53 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi Urzula,
>
> I'll give you an example. These are "restraints" and not "constraints".You
> have to have a separate restraint file that looks like below.
>
> &rst iat=15360,15377, r1=0.0, r2=13.8, r3=13.8, r4=100.0, rk2 = 10.0,
> rk3 = 10.0, /
>
> The above restraint file says
>
> 1) The distance restraints will be applied to the distance between atom
> 15360 and atom 15377
> 2) The shape of the potential has been changed from a "U"shape to a
> harmonic shape by making r2 equal to r2.
> 3) The minimum of the harmonic potential is at r2=r3=13.8 Angstrom
> 4) The force constant is 20 kcalmol-1A-2 (because Amber regards 0.5K as
> the constant)
> 5) The potential will be harmonic from distance = 0A to distance=100A,
> beyond that it would increase linearly.
>
> In you amber input file you have to have
> DISANG=name of the above restraint file
> DUMPAVE=name of the distance output file (the values of the distance will
> be written to this file as the MD simulation continues)
>
> Hope this helps
>
> Sajeewa
>
>
> On Wed, Apr 2, 2014 at 9:33 AM, Urszula Uciechowska <
> urszula.uciechowska.biotech.ug.edu.pl> wrote:
>
>> Dear Amber users,
>>
>> I am trying to apply distance constraints between the residue of my
>> portein and nuc.acid of my DNA molecule. Can someone suggest me how should
>> I start.
>> I went through the Tutorial 4 but do not know how to relate it to my case.
>> Sould I prepare 7colum file?
>> Could anyone suggest me something?
>>
>> Thank you
>>
>> best regards
>> Urszula
>>
>>
>> -----------------------------------------
>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> http://www.ug.edu.pl/
>>
>>
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>
>
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Received on Wed Apr 02 2014 - 08:00:03 PDT
