Re: [AMBER] Wrong number of restrained atoms

From: David A Case <>
Date: Thu, 3 Jul 2014 08:22:47 -0400

On Thu, Jul 03, 2014, Valentina Romano wrote:
> My protein-atom complex goes to residue 269 to 525 (2065 atoms).
> But checking the output file I notice that only 771 atoms are restrained.

You can use the "ambmask" program to see what atoms correspond to a given
mask. (Type "ambmask" to see help on how to use the program; in this case,
give ':269-525' as your mask.)

As a wild guess: Amber renumbers residues starting from 1. You have to use
the Amber residue numbers (and not the original numbers, if they are


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Received on Thu Jul 03 2014 - 05:30:03 PDT
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