Re: [AMBER] missing loop

From: Sergio R Aragon <>
Date: Tue, 3 Sep 2013 21:58:16 +0000

Hello Fabian,

One of the nicest tools to add missing residues to a structure is Modeller. You can obtain it free here:

Please follow the tutorials to learn how to use the program. Once you have a finished structure from modeler, you need to proceed to add the aa loop region (replace some that overlap with your original structure on either loop end) to your original pdb file and continue the rest of the process with the program leap (say tleap for the text version) so that you can prepare input files for pmemd for MD. 12 missing residues will be a simple task with this program.

If your protein has no metals, the rest will be easy. If there are metals, you may have to ask for help again from this list.

Good luck,

Sergio Aragon
Professor of Chemistry, SFSU

-----Original Message-----
From: Fabian Glaser []
Sent: Tuesday, September 03, 2013 7:06 AM
To: AMBER Mailing List
Subject: [AMBER] missing loop


I am interest in using amber to study the protein in PDB 3cio. But it has a 12 aa loop missing, which cannot be modeled using similar structures. I wonder what would be the best strategy to model this loop, or alternatively how to simulate this protein dynamics.

Thanks a lot,

Fabian Glaser,
Technion, Israel

Fabian Glaser, PhD
Bioinformatics Knowledge Unit,
The Lorry I. Lokey Interdisciplinary
Center for Life Sciences and Engineering

Technion - Israel Institute of Technology
Haifa 32000, ISRAEL
Tel: +972 4 8293701
Fax: +972 4 8225153

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Received on Tue Sep 03 2013 - 15:00:03 PDT
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