In xleap, I do something similar to:
(cen = my central residue, arm1 = first side chain, arm2 = a second
side chain, etc.)
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 }
...and so on...
Of course, this assumes that arm1, arm2, etc. have "head" set.
Hopefully this makes things a little clearer. I found myself mucking
around in xleap a few times before I got everything just right, but
then it's pretty easy. Always look at the structures (edit tmp1, tmp2...)
and save things using saveoff when you get it right. Also, the
leap.log file can be useful for documenting what you did that actually
worked :-)
As for atom types, you want to define these according to the final,
assembled structure that you will be doing dynamics on.
I find the trickiest thing in setting up custom residues in Amber is
how to handle charges/charge generation since they usually have
dangling bonds. Obviously, one uses capping groups of some sort, but
then it is not well determined how you cut off these capping groups
while producing sane per-residue charges.
Hope this is of some help - John
On Mon, 23 Feb 2004 opitz.che.udel.edu wrote:
> Sorry, I am thinking in steps today. The previous residues I used to read
> in a pdb file, but looking at the pdb output from that, there is a
> mistake. Now, my question is, if I follow the description below, how do I
> connect the respective residues in leap? How do I make one molecule out
> of it that I can then define as a new residue to attach something else too?
> Thanks,
>
> Armin
>
> ==============Original message text===============
> On Mon, 23 Feb 2004 15:44:44 EST John Bushnell wrote:
>
> I built some polymers with a tetrahedral core where I needed to
> make a series of connections to the central unit. What I did
> was to define a tail, connect a side-chain to it, then redefine
> another tail, connect to that, etc. I believe that you can define
> a tail as many times as you want, but it will be set to whatever
> the last atom you set it to. As already suggested, 'desc' is your
> friend in leap.
>
> - John
>
> On Mon, 23 Feb 2004 opitz.che.udel.edu wrote:
>
> > I did find the problem that I had, but I still have 2 tails in the
> > residue and it doesn't give me an error. Is it possible that residues can
> > have 2 tails or is it just not telling me that there is a problem?
> > Also, if I can only define one tail, how can I effectively make a residue
> > that has 2 tails?
> > Thanks,
>
>
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Received on Mon Feb 23 2004 - 22:53:00 PST
