AMBER Archive (2004)

Subject: Re: AMBER: Star like (branching) molecule

From: John Bushnell (
Date: Tue Feb 24 2004 - 17:33:45 CST

I used the method below to create a branched oligomer, and
succesfully attached four arms to a single central atom, in
some cases using the same "arm" residue for all sidechains.
I did this from within xleap, and checked that the structures
that I was creating were reasonable (and correctly bonded) using
the edit command. I then saved each final structure using the
saveoff command in case I wanted to modify them later. And
finally used the saveamberparm command to produce .top and .crd
files for subsequent dynamics. I did not create any pdb files
from within xleap, as I really didn't have much use for them.
I just needed the .top/.crd files for running Amber. And I
usually just use a local script that utilizes the 'anal' Amber
utility to convert coordinate files to pdb's in order to visualize
results. So I never even considered what a pdb file would look
like as you mention. Once I have good top/crd files in hand, I'm
usually happy.

    - John

On Tue, 24 Feb 2004 wrote:

> 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.
> Thanks,
> Armin
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