Re: [AMBER] SCEE and SCNB GLYCAM_06 values with amber11 top crd files

From: David A Case <>
Date: Wed, 18 Apr 2012 15:10:00 -0400

On Wed, Apr 18, 2012, Kepa K. Burusco wrote:
> I have checked the amber reflector archives, amber tools manuals 11 and
> 12, and amber manuals 9, 10 and 11 and I have found different comments
> regarding SCEE and SCNB so I still have doubts.

I'm not surprised: the way scee and scnb are handled has been evolving.
Stick with AmberTools12 and its instructions, as far as running LEaP. You
should not need any "write14scale" commands, as that is automatically done.

Then, examine the prmtop file to see if you got the values you want.

You can use Amber11 executables like sander or pmemd in conjunction with
prmtop files created with AmberTools12. Again, it's good to run some short
sanity checks to make sure you are getting what you expect.

See for
a useful discussion of using Amber11 programs alongside AmberTools12.

...good luck...dac

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Received on Wed Apr 18 2012 - 12:30:03 PDT
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