AMBER Archive (2004)

Subject: AMBER: protein-carbohydrate complex

From: Mikyung Seo (seo_at_ualberta.ca)
Date: Thu Apr 22 2004 - 17:27:31 CDT

Thanks for your reply.
However, I still have questions.

I divided into each protein and carbohydrate pdb file from whole complex pdb
file.
I created prep file for my carbo using antechamber with charges=0.
(because I want to use resp charges from Woods' parameters)
Do I need to add resp charges for carbo manually?
Antechamber seemed to assign atom type with parm94 parameters for carbo.
Is there any way for antechamber to read glycam parameters for carbo?

In xleap, I loaded carbo prep file and loaded protein pdb file.
And then I combined them using combine command.
However, when I open whole system with unit editor sugar is located too far
from protein and some bonds are broken. It is supposed to be close to protein.
What is wrong with prep file? Doesn't antechamber read coordinates correctly?

I also tried to load each pdb file for protein and sugar.
In this case, sugar structure is not represented correctly.
It has some dots and broken bonds.

Could you help me to slove these problems?
Thanks.

Mikyung

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu