AMBER Archive (2005)

Subject: RE: AMBER: capping?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Mar 08 2005 - 20:09:44 CST

Dear Gavin,

You can simply take the pdb of your uncapped system and at the correct end
simply add a single atom for ACE and then at the other end a single atom for
NME. When you then load the pdb in xleap it will add the missing atoms. You
just need to pick reasonable coordinates for the two atoms you add.

You can then manually select these atoms and use xleaps relax command to get
a reasonable starting structure that you can then minimise in sander. This
is very similar to the "fake" pdb I talk about in the following tutorial:

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_Six/index.htm

The difference is that between the ACE and NME residues you will have the
system that you want to have capped.

I hope this helps. If you have problems get back to me with your pdb file
and I'll see if I can explain it better.

All the best
Ross

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|\oss Walker

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Hui-Hsu Tsai
> Sent: 08 March 2005 13:35
> To: amber_at_scripps.edu
> Subject: AMBER: capping?
>
>
> Dear Amber Community,
>
> I am doing simulations of short peptides which required to be
> acetylated
> and amidated at N and C termini.
> Is there any one here can give me some suggestions how to
> perform capping
> in Amber? I would like to cap the peptides with Ace and Nme.
> I am a new
> amber user. Any suggestion is appreciated. Thanks.
>
> Gavin
>
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