Re: AMBER: problems in adding ACE and NME group

From: backy <backy.ibms.sinica.edu.tw>
Date: Mon, 25 Jun 2007 21:21:47 +0800

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" <case.scripps.edu>
To: <amber.scripps.edu>
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
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
>
> --
> No virus found in this incoming message.
> Checked by AVG Free Edition.
> Version: 7.5.472 / Virus Database: 269.9.1/857 - Release Date: 2007/6/20
> ¤U¤È 02:18
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jun 27 2007 - 06:07:19 PDT
Custom Search