(unknown charset) Re: Re: [AMBER] minimization really make protein better?

From: (unknown charset) geyan <geyan.big.ac.cn>
Date: Tue, 30 Mar 2010 11:15:55 +0800

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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 29 2010 - 20:30:02 PDT
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