AMBER Archive (2004)

Subject: Re: AMBER: Defining residues

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Feb 23 2004 - 16:39:48 CST

> set cen tail cen.1.x (where x is the tail atom number)
> tmp1 = sequence { cen arm1 }
> set tmp1 tail tmp1.1.y (where y is where I want to attach arm2)
> tmp2 = sequence { tmp1 arm2 }
> set tmp2 tail tmp2.1.z (z is the new tail on the central residue)
> tmp3 = sequence { tmp2 arm3 }

Have you verified that the parts are actually bonded?

Using 'sequence' should guarantee that leap will try to orient
the joined residues according to internal coordinates derived
from the residue templates (i.e. trying to keep atoms being
bonded oriented properly for ther hybridization), however there
is no guarantee that steric overlap will be avoided.

Another approach is to put together a pdb file with all parts aligned
with TER cards between them using a more powerful graphical editor
than leap, then loadpdb and use the 'bond' command in leap to join them.

Bill
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