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 - 15:13:20 CDT

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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