[AMBER] Keeping an hexamer whole.

From: Julio Dominguez <acheron24.hotmail.com>
Date: Thu, 5 Dec 2013 00:38:16 +0000

Dear amberists,

We are simulating a hexamer with six ligands but we are unable to make a "movie" of the complex in the proper oligomeric form. That is, we have fail in our attempts at centering all the subunits and ligands.

We have use the autoimage, center and image commands in various combinations (within cpptraj):

1) autoimage

2) center :1-1602 mass origin
   image origin center

3) center :1-1602

4) center :1-1602 origin
   image origin center familiar

5) center :1-1602 origin
    image origin center familiar

I believe the second command gave the best results. Am I missing something? Any suggestions? 

Best regards.
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Received on Wed Dec 04 2013 - 17:00:02 PST
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