AMBER: MD for protein-carbohydrate complex

From: Mikyung Seo <>
Date: Thu, 22 Apr 2004 14:03:33 -0600

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

Any comments will be helpful.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Apr 22 2004 - 21:53:00 PDT
Custom Search