AMBER Archive (2004)

Subject: AMBER: MD for protein-carbohydrate complex

From: Mikyung Seo (seo_at_ualberta.ca)
Date: Thu Apr 22 2004 - 15:03:33 CDT

Hello Amber users,

I am performing MD on protein and carbohydrate complex.
I just started to use AMBER 7.0

My pdb file contains protein and Abe(Man)Gal trisacchride.
In xleap, do I need to load whole pdb file including protein-carbohydrate
complex and save it as top and crd files for Sander?
In this case, how can I assign charges for carbohydrate?

or do I load each molecule separately and save it into different top file for
Sander? i.e. load pdb file with only protein and load prep files for
trisacchride?

Any comments will be helpful.
Thanks.
Mikyung

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