AMBER Archive (2003)

Subject: AMBER: combine prep files

From: Mi-Kyung Seo (mkseo98_at_hotmail.com)
Date: Tue Jul 29 2003 - 16:14:52 CDT

Dear Amber users,

I am trying to perform MD for carbohydrates with AMBER 7.0
I want to combine and make polysacchrides with Woods each carbohydrate prep
fragment. (from Glycam web)

I tried "combine" and "bond" command in XLEaP but I can't open combined prep
and structure is not correct.

Second thing,
When I build new molecule and save it using "saveamberprep" in XLEaP, prep
file format is different from Woods prep format. It uses cartesian
coordinates and no bond information.
Are there 2 kinds of prep file formats, cartesian coord. and z-matrix
format?
or Is there any way to convert cartesian coord. to z-matrix format?

I'd appreciate any help.
Thanks.
Mikyung

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