Hello Mehdi!
Your RST file would be something like this:
### Restraints par 1-34
&rst
iat=1,34,
r1=27,
r2=27.5,
r3=27.5,
r4=28,
rk2=5.0,
rk3=5.0,
/
where 27, 27.5 and 28 is the distance of separation and 5.0 is the harmonic
constant. Page 103 of the Amber manual has all the specifics.
Remember that separating two base pairs in a DNA chain would result in a
"zipper" like conformation so the sampling will be different for each
distance.
Hope that helps!
Rodrigo.
On Sat, May 12, 2012 at 9:18 AM, mehdi bagherpoor <ms.nightsky.gmail.com>wrote:
> Dear all
>
> I am using Amber software for DNA simulation (Amber10). Specially in my
> project I need to exert external force between two residue to these two
> residue separate from each other.
>
> The DNA that I want to simulate has 17 bp and I need exert external force
> between 1 and 34 residues to these
> two residue separate from each other.
>
> I will use umbrella sampling. but I don't know how write dist.RST file?
>
> Now I am wandering if you could advise me a method.
>
> I would appreciate your help.
> Looking forward to hearing from you.
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>
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Received on Sat May 12 2012 - 08:00:02 PDT
