Thanks!
I need to prepare ATP-prot complex for MD. Actually I have ATP docked into
protein binding site.
May I just open that parameter file in Schrodinger and manually superimpose
it with the old ATP ligand?
Or should I do something else?
Additional question: how to prepare Mg-ATP-prot complex? May I just add
Mg(2+) into solvent?
On Tue, Jun 21, 2011 at 5:05 PM, Takeshi Baba
<tbaba.cheng.es.osaka-u.ac.jp>wrote:
>
>
> > Hi All,
> > Does anybody have experience of preparing ATP structure by
> > Antechamber?
> > I tried to use mol2 file generated as by MOE as by Schrodinger, but
> > never
> > had luck to solve this question.
> >
>
> You should check http://www.pharmacy.manchester.ac.uk/bryce/amber
> There is amber parameter of ATP.
>
>
> ----------------------------------------------------------------------------------------------------
> Takeshi Baba
>
> Graduate School of Life Science, University of Hyogo,
> 3-2-1 Koto, Kamigori, Akoh-gun, Hyogo 678-1297, Japan
> E-mail: tbaba.cheng.es.osaka-u.ac.jp
>
> ----------------------------------------------------------------------------------------------------
>
>
>
>
>
>
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>
--
Best regards,
Azat Mukhametov, PhD
Centre for Chemical Biology at Universiti Sains Malaysia (CCB.USM)
1st Floor, Block B,
No.10, Persiaran Bukit Jambul,
11900 Bayan Lepas,
Penang, Malaysia.
http://www.ccbusm.com
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Fax : +604-6535514
email: azatccb.gmail.com
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Received on Tue Jun 21 2011 - 02:30:04 PDT
