From: Jason Swails <>
Date: Sun, 28 Jul 2013 19:38:32 -0400

On Sun, Jul 28, 2013 at 5:50 PM, Shashidhar Rao <>wrote:

> Thanks, Jason. I did not explicitly provide a receptor_mask. I assume in
> my case, it would be :1-342

> I looked at the log file and its best guess seems to have worked well. I
> will check and the results and see if they make sense.

In my opinion, you should always use the default mask guesser. There is
really only one case in which I know it will fail, and that's if the ligand
is made up of multiple residues that are separated by residues in the
receptor. This could happen in a dimer, for instance, or if you are
including different water molecules as ligands. The mask guesser will not
be able to guess a ligand mask like


Also, if you have multiple ligand residues (like, for instance, with
Hemoglobin that has 4 binding sites), you may need to use "receptor_mask"
and "ligand_mask" if you want to specify a particular ligand to treat as
the 'ligand' in (By default, the last ligand will always be
chosen using the default mask guesser).

Outside of these two scenarios the default mask guesser should be correct.
 Using the default masks often exposes inconsistencies in the underlying
topology files that would otherwise be difficult to correct, so unless you
know for certain that the default masks are wrong for one of the two
reasons listed above, it's probably best to use the mask guesser by default.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jul 28 2013 - 17:00:02 PDT
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