AMBER Archive (2006)

Subject: AMBER: Combining Residues in LEaP for Lipid Bilayers

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Mon Nov 20 2006 - 11:09:13 CST

Everyone,

I'm trying to create LEaP scripts to build custom sized lipid bilayers.
I've been able to build a bilayer using Leap and fragments of lipids (head,
middle and tail groups) but I can't seem to combine the residue names in the
output files. For example, I've built a DMPC bilayer using head
(phosphocholine), middle (glycerol) and tail (myristoyl) groups. I start
off with 4 units for each of the groups (the DMPC tail groups are the same
but have different unit names) and attach them together using the head and
tail commands. Each of these four units has a corresponding residue name.
Once the units are combined together, they still retain their original
residue names. I'm trying to combine the four residue names into one
residue name in the each lipid unit but I can't see to get that to work
using the 'combine' statement. Does anyone have any suggestions or
comments? Should I treat each of the 4 starting units as residues and use
the connect0 and connect1 commands?

 

Thanks,

 

Matt Tessier

Woods Lab

Complex Carbohydrate Research Center

University of Georgia

matthew.tessier_at_gmail.com

 

 

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