Re: AMBER: modified leaprc for glycoproteins

From: David A. Case <>
Date: Fri, 31 Aug 2007 14:42:03 -0700

On Fri, Aug 31, 2007, Irene Newhouse wrote:
> The system I'm trying to simulate contains both glycans and protein. None of
> the supplied leaprc files manage to do both. [OK, I didn't try them all, but
> I did try the ones that seemed obviously named to me]. So I tried to create
> my own, by combining leaprc.glycam04 and leaprc.ff99SB. That doesn't work
> either - it loads the protein file, but not the glycam04 file.

Exactly how did you "combine" them? You should be able to type the following
in leap:

source leaprc.ff99SB
source leaprc.glycam04

That gets all of the files loaded; there may be other problems down the road.
You might want to check out the glycoprotein configuration tool at -- that could be what you need, or could give to hints about how
to proceed.


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Received on Sun Sep 02 2007 - 06:07:37 PDT
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