AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Mon Jun 25 2007 - 09:01:52 CDT

you can use xleap to add ACE and NME to cap the system

backy <backy_at_ibms.sinica.edu.tw> wrote: Actually, how users cap the protein terminal?
For example, by which kind of program to put the initial coordinates for ACE
and NME groups?

backy
----- Original Message -----
From: "David A. Case"
To:
Sent: Thursday, June 21, 2007 1:10 PM
Subject: Re: AMBER: problems in adding ACE and NME group

> On Thu, Jun 21, 2007, backy wrote:
>
>> If there is a need in placing the whole ACE and NME group, how should I
>> input their initial coordinations?
>
> This is a very rare thing to do, and Amber admitedly doesn't make it very
> easy. It isn't something I would recommend just "for practice".
>
> You might use a homology-modeling program to add alanine at both ends,
> then
> delete the atoms you don't need, and change the residue names to ACE and
> NME.
>
> ....dac
>
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