Re: [AMBER] : Dimer Imaging Problem

From: Waldner, Birgit <>
Date: Wed, 11 Mar 2015 16:41:00 +0000

Thank you, that solved the problem :).
From: Daniel Roe []
Sent: Wednesday, March 11, 2015 5:31 PM
To: AMBER Mailing List
Subject: Re: [AMBER] : Dimer Imaging Problem


Does 'autoimage' by itself work?


On Wed, Mar 11, 2015 at 10:28 AM, Waldner, Birgit
<> wrote:
> Dear Amber users,
> I'm having trouble imaging a dimer that consists of two not covalently linked monomer units and is glycosylated at the interface of the two units. I use a 12A octahedral box for solvation. Residues 1-221 and 222-442 are the protein monomers and residues 442-436 are the oligosaccharide chains.
> When I image it using the following syntax:
> center :1-221 origin
> image origin center familiar
> center :1-436 origin
> image origin center familiar
> I see glitches when I look at the trajectory, meaning that most of the time the monomer units are close together as they should be, but at some points the two monomer units are at opposite ends of the box.
> I also tried using autoimage with:
> autoimage :1-436 origin familiar, but I get an error message, because it is not just one molecule to autoimage and in the resulting trajectory the monomer units are at opposite ends of the box all the time.
> Am I using the autoimage command wrong or do you have any other suggestions? Thank you for your help.
> Best regards,
> Birgit
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Mar 11 2015 - 10:00:02 PDT
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