AMBER Archive (2007)

Subject: AMBER: Example needed for addAtomType command

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Feb 01 2007 - 15:26:12 CST

I'm interested in understanding how to add a different atom type to use
with xLeap. I'm using Amber 8. I looked at the manual and found the
command is addAtomType and you need to define the type and the
hybridization. However, I'm not sure how to apply it. I've found in
the past that by looking at the tutorials and comparing the examples of
the commands there with the more technical information in the manual
really helps me understand.

Could someone give me an example of how and where I'd use this?

For example: say I wanted to add a sp3 hybridized carbon (I know that
it already exists, I'm just trying to understand the concept with an
example), how and where is it entered?

Thank you so much,

Kara Di Giorgio
Graduate Student
University of the Pacific

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