From: chengh_at_ringo.chem.pitt.edu
Date: Thu Feb 11 2010 - 11:51:54 CST
Dear Chris,
Many thanks for your reply. Regarding the positional restraints, can I
just use "constraints on" and put 1Kcal/mol to restrain the ion? If I am
only interested in the different solvation energy in the water and
protein, restraining the ion in both water and protein might cancel the
entrop effects. Right?
Thanks again,
Mary
> Dear Mary,
>
>
> there is of course a need to include positional restraints as the
> ion is being grown in protein, because at λ = 0, when the two do
> not interact, the former is free to move astray far from the binding
> site. Positional restraints can be enforced, for instance, using the
> keyword extraBonds in NAMD or the Colvars module. Be aware, however,
> that enforcing such restraints is tantamount to a loss of translational
> entropy, which, accordingly, ought to be measured in terms of free
> energy. Luckily, in the case of an ion, this quantity can be evaluated
> analytically rather easily. This problem is being dealt with in the
> new version of the FEP tutorial, which is either already out, or will
> be so very shortly.
>
>
> Chris
>
>
>
> chengh_at_ringo.chem.pitt.edu a écrit :
>> Hi all,
>>
>> I am using FEP to calculate the binding energy of Na ion inside the
>> protein. I did not put any restraint on the ion and observed that later
>> on
>> this ion moved away from the binding site. This ion is supposed to
>> disappear finally. Should ion's moving away from the binding site affect
>> the binding energy? I think I may need to restrain it. Any suggestion?
>>
>> Thanks,
>>
>> Mary
>>
>>
>>
>
>
> --
> _______________________________________________________________________
>
> Chris Chipot, Ph.D.
> on leave from Nancy Université, CNRS
> Theoretical and Computational Biophysics Group
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 North Mathews Phone: (217) 244-5711
> Urbana, Illinois 61801 Fax: (217) 244-6078
>
> E-mail: chipot_at_ks.uiuc.edu
> Christophe.Chipot_at_edam.uhp-nancy.fr
> Web: http://www.ks.uiuc.edu/~chipot
> http://www.edam.uhp-nancy.fr
>
> I disapprove of what you say, but I will defend to the death your right
> to say it
> Evelyn Beatrice Hall
> _______________________________________________________________________
>
>
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