AMBER Archive (2006)

Subject: RE: AMBER: Combining Residues in LEaP for Lipid Bilayers

From: kepa koldo burusco (
Date: Fri Nov 24 2006 - 05:38:06 CST


Hi Matt,

I think I had a sort of problem quite "similar" or at
least "related" to this one you have. I tried to build
a solvent box entirely made of the same molecule. This
molecule was made of different units so, when I tried
to create the solvent, xLEaP complained because it
expected a single unit molecule as a solvent (there is
a hint about this at AMBER 7 manual, on page 199,
solvent command, first paragraf).

Maybe if you try to build your molecules in a single
piece (a single unit) you could avoid this problem...
It worked with my problem, although I would have
preferred to built my molecules by pieces (
"modularity is fantastic... whenever it works... ;-)
..." )...

Good Luck!!!

Kepa K. Burusco

PhD Student
Department of Chemistry.
Universidad Autónoma de Barcelona


 --- Matthew Tessier <>

> 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

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