AMBER Archive (2007)

Subject: AMBER: modified leaprc for glycoproteins

From: Irene Newhouse (einew_at_hotmail.com)
Date: Fri Aug 31 2007 - 15:53:05 CDT

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.
 
I've seen messages in the archives that indicate others have solved this problem, but not how.
 
When I search for "glycoprotein" in the manual, there's nothing.
 
Thanks for you help!
 
Irene Newhouse.
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