AMBER Archive (2006)

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

From: Dave, Sonya (sonya.dave_at_vanderbilt.edu)
Date: Wed Oct 25 2006 - 16:41:48 CDT

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 simulation would that 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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