I just want to prevent the unfavourable electrostatic and h-bond interaction
between free phosphate tail and residues of the side. The idea is that ion
should provide such ATP conformation...
24 октября 2011 г. 15:34 пользователь Gannett, Peter
<pgannett.hsc.wvu.edu>написал:
> As to the second question, depends on what you want to know. However,
> constraining things, I think, should be done with caution.
>
> Pete Gannett
>
> ________________________________________
> From: Алексей Раевский [rayevsky85.gmail.com]
> Sent: Monday, October 24, 2011 8:30 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] ATP+Mg
>
> Yes I think so too. Thank you for reply. Can I ask you? Do you have any
> suggestions about second problem???
> Sorry for such obsession!
>
> 24 октября 2011 г. 14:18 пользователь Gannett, Peter
> <pgannett.hsc.wvu.edu>написал:
>
> > Maybe it would be easier (better) to use the ATP parameters that have bee
> > posted at:
> >
> > http://www.pharmacy.manchester.ac.uk/bryce/amber#cof
> >
> > Pete Gannett
> >
> > ________________________________________
> > From: Алексей Раевский [rayevsky85.gmail.com]
> > Sent: Monday, October 24, 2011 3:59 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] ATP+Mg
> >
> > Hi all. I need your advices about my task which is closely associated
> with
> > ATP toplogy in the binding site. As I understood from one of the letters
> (
> > http://archive.ambermd.org/201106/0522.html) I can use antechamber or
> > derive
> > charges from the site linked in the letter. But the ATP's phosphate tail
> is
> > very flexible and very negatevly charged thus I need too coordinate it
> with
> > Mg ion to prevent an increased flexibility and motion. Here are some of
> my
> > questions:
> > 1. What parts of initial structure I have to prepare and process with
> > antechamber - separate adenylate and metal or both of them together like
> a
> > compound?
> > 2. After getting separate topologys / complex topology - is it necessary
> to
> > constrain the distances between PO2 groups and metal to be sure this tail
> > won't move anyway during MD or this coordination bond is strong enough?
> >
> > Thank you
> > --
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>
>
>
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Received on Mon Oct 24 2011 - 06:30:02 PDT
