AMBER Archive (2009)

Subject: Re: [AMBER] Re: join two units in amber9 or amber10

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Mar 16 2009 - 17:56:01 CDT

> A while back i asked about creating a bond between two units in xleap.
> In the manual there is a combine command that can combine two or more
> units into one and then i can use the bond command to create the bond.
> my question is how does xleap (AMBER) decide on the orientation when
> combining two units?

It might just superimpose centers of geometry. I would be inclined
to make a pdb file with the units oriented as desired, using the
program of choice, then loadpdb to get it in leap. Remember to put
a TER 'card' between the residues in the pdb if they are not bonded
at load time. After loading, add the bond you want in leap via cmd line
or drawing in the edit window.

Bill

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