RE: AMBER: capping?

From: Ross Walker <>
Date: Tue, 8 Mar 2005 18:09:44 -0800

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:

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

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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> -----Original Message-----
> From:
> [] On Behalf Of Hui-Hsu Tsai
> Sent: 08 March 2005 13:35
> To:
> 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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Received on Wed Mar 09 2005 - 02:53:01 PST
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