AMBER Archive (2004)

Subject: AMBER: Star like (branching) molecule

Date: Tue Feb 24 2004 - 16:54:45 CST

('binary' encoding is not supported, stored as-is) Yesterday I had asked how to build a star like molecule if only 1 tail
can be defined.
I got the very useful suggestion to define my system the following way:

(cen = center, arm1 = first side chain, arm2 = second side chain, etc.)

set cen tail cen.1.x
tmp1 = sequence {cen arm1}
set tmp1 tail tmp1.1.y
tmp2 = sequence {tmp1 arm2}
set tmp2 tail tmp2.1.z
tmp3 = sequence {tmp2 arm3}

And at first it appeared to work. But when I tried to add the second arm
(which attaches to the same atom as the first arm, and has the same
structure as the first arm) the pdb file I obtained had TER cards between
the seperate residues. This was not the case after adding the first arm
to the center.
What is the problem? Is it that I can't attach it to the same atom? Can
the second arm NOT be of the same structure as the first arm?
Help is very appreciated. I would especially like to hear from the person
that had suggested this, if they had this problem how they solved it.


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