Dear Amber users,
I would like to also ask if anyone could suggest me if its better to put the restrains already at the begining of MD simulation, minimization steps or later? I am new to this..
Thank you in advance for help
/Urszula
________________________________________
Von: Brian Radak [radak004.umn.edu]
Gesendet: Donnerstag, 15. März 2012 14:59
An: AMBER Mailing List
Betreff: Re: [AMBER] puting restrains
Hi Urszula,
You would really have to check the literature for such things (I'm not
really an expert on proteins, perhaps someone else can suggest specific
references). A rather ambiguous question: Do you want strong or gentle
restraints? In my experience/opinion, a "strong" restraint would be around
100-500 kcal/mol-A^2, but that doesn't really mean anything in general.
A technical note, I believe the nmropt and ntr flags uses the restraint
form U(x) = k(x - x_ref)**2, whereas the NCSU modules use the form U(x) =
0.5k(x - x_ref)**2.
Regards,
Brian
On Thu, Mar 15, 2012 at 9:24 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> Dear Amber users,
>
> I would like to put some restraints on residues in my protein between the
> Val270-Ala357 and Asn78-Phe180. Could someone suggest me what force value
> should I use to keep those chains in kind of stable position? Attached is
> the protein that I am going to use in MD.
>
> /Urszula
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Mar 16 2012 - 04:30:03 PDT
