AMBER Archive (2006)

Subject: RE: AMBER: How do we simulate deletion mutations

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Oct 25 2006 - 17:43:49 CDT

Your methods should be workable. Then just use it as a
kind of regular PDB file and start to get the parmtop
and inpcrd files.

Computational modeing is to use Swiss-Model or some
other software to get the PDB file of the deleted
protein with your original PDB file as template.

Best regards.

Fenghui Fan

--- "Dave, Sonya" <sonya.dave_at_vanderbilt.edu> wrote:

> Hi,
>
> Thanks for the suggestion. Can I clarify it? How
> am i supposed to "use computational modeling to get
> the PDB file of the deleted protein"? What sort of
> thasimulation would t be? I was planning to, in the
> pdb file, delete the lines corresponding to the
> amino acids. Then what?
>
> Thank you,
> Sonya
>
> ________________________________
>
> From: owner-amber_at_scripps.edu on behalf of Fenghui
> Fan
> Sent: Wed 10/25/2006 3:13 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: How do we simulate deletion
> mutations
>
>
>
> My way to do that is to use computational modeling
> to
> get the PDB file of the deleted protein, then run
> sander.
>
> Best regards.
>
> Fenghui Fan
>
> --- "Dave, Sonya" <sonya.dave_at_vanderbilt.edu> wrote:
>
> > Hello,
> >
> > I have a protein segment which is about 70 a.a. I
> > have the crystal stucture model. In amber, is
> there
> > a way to simulate the effect of deleting 17 of
> those
> > amino acids(the 17 are continuous)? If not amber,
> > are there any other programs that will do it? How
> > would I approach this?
> >
> > I also want to get simulate the effect of deleting
> > those amino acids in a simulated (not crystal
> > stucture) version of a similar protein segment.
> >
> > Thanks,
> > Sonya Dave'
> >
> > ________________________________
> >
> > From: owner-amber_at_scripps.edu on behalf of Elijah
> > Gregory
> > Sent: Tue 10/24/2006 6:17 PM
> > To: amber_at_scripps.edu
> > Subject: Re: AMBER: Not getting proper structure
> > after minimization
> >
> >
> >
> > As far as parameter sets.... you should know that
> > most forcefields out
> > there overemphasize alpha-helix structure....
> it's
> > trickier to
> > simulate alpha/beta structures. Look in the
> > literature for *anything*
> > done with MD and your protein (or related
> > homologues) for more hints
> > and tricks. MD is not easy, but nothing ever is
> =P
> >
> > ~Elijah
> >
>
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> >
>
>
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