it's generally not possible to just take a homology model., put it it water
and have it improve with minimization.
this is an open research problem. you might want to look at papers in the
literature and follow the protocol that they used.
On Mon, Mar 29, 2010 at 11:15 PM, geyan <geyan.big.ac.cn> wrote:
> I am sorry to have asked a unclear question.
> Now I attach the initial and minimized protein structure and their
> prochecked result with the corresponding name.The initial one is produced by
> Modeller.I used the Amber9 with the ff99SB force field and add Na+ to keep
> neutralized and solvate the protein with TIP3PBOX 9.0.Then do the
> minimization with two steps.First step,keep protein fixed and minimize the
> water and ions and the second step is keep the protein backbone Ca fixed and
> minimize the whole system,detailed parameter as follows.
> Minimization of the water and ions
> &cntrl
> imin=1,
> maxcyc = 5000,
> ncyc = 250,
> ntr = 1,
> cut = 12
> ntpr=5,
> drms=0.005,
> &end
> Keep protein fixed with weak restraints
> 100.0
> RES 1 75
> END
>
> Minimization of the entire molecular system
> &cntrl
> imin=1,
> maxcyc = 5000,
> ncyc = 250,
> ntr = 1,
> cut = 12
> ntpr=5,
> drms=0.005,
> &end
> Keep Ca fixed with weak restraints
> 10.0
> FIND
> CA * * *
> SEARCH
> RES 1 75
> END
> END
>
> Hope now the information is clear.
> Thanks all!
> 2010-03-30
>
>
>
> geyan
>
>
>
> 发件人： Carlos Simmerling
> 发送时间： 2010-03-29 19:36:17
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] minimization really make protein better?
>
> you don't give us enough information to help you.
> what was the initial structure? how was it generated? (xray, NMR, model,
> random guess?)
> what amber version, what force field, what conditions, what kind of
> minimization?
> On Mon, Mar 29, 2010 at 12:48 AM, geyan <geyan.big.ac.cn> wrote:
> > Hi,
> > I have met a strange phenomenon.The structure I have minimized with
> Amber
> > looks somewhy worse than origin
> > which can be seen clearly from the Procheck,a software that is used to
> > check the protein's 3D structure.The percentage of residues in most
> favoured
> > regions decline notably.It seems a little unbelievable to me,what do you
> > think?
> > Any suggestions will be appreciated.
> > 2010-03-29
> >
> >
> >
> > geyan
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Mar 30 2010 - 04:30:05 PDT
