[AMBER] defining the mixed 1-4 scaling in amber 11 and sleap

From: Toshifumi Yui <tyui.cc.miyazaki-u.ac.jp>
Date: Thu, 3 May 2007 21:18:52 +0900


My system is the complex of protein and carbohydrate molecules, which are
not covalently connected.

I wish to implement a job with different SCEE and SCNB values in pmemd of
amber11, if possible (Unit value for carbohydrate and the default ones for
Here is my sleap input file.

>sleap -s -f
>set default write14scle on
>source leaprc.ff99SB
>source leaprc.GLYCAM_06

>model = loadPdb comp.pdb
>saveamberParm model comp.parm7 comp.inp

Unfortunately, it seems not to work appropriately, and probably the default
scaling factors have been only assigned to all of the parameters.
I wonder if I am wrong in this regards.

Thank you.

Toshi Yui

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Received on Tue May 03 2011 - 06:00:02 PDT
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