AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Nov 21 2006 - 10:16:06 CST

On Mon, Nov 20, 2006, Matthew Tessier wrote:

> 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.

>
> #Combining the different residue units into one name
> DMP = combine { 1PC 3GY MYR MY2 }

After this, I *think* you want to save the DMP unit as an off or mol2 file.
Then, in a separate leap run, you can read it in, and all of the atoms will
have the residue name DMP. (You can look at the saved files to be sure of
what it is doing, or to change something you don't like.)

...hope this helps...dac

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