Re: AMBER: Re:tree name generated by tleap is different from the input PREP parameter file

From: Bill Ross <>
Date: Tue, 2 Jan 2007 20:26:14 -0800 (PST)

> 1)How one can select correct atoms as that one want in the constrained group
> according to group names such as "* * S *" ?

The tree type assignment is not unique (there are usually multiple
possible combinations of tree types combined with LOOP closure pairs).
I.e. ultimately there is no such thing as an 'S' (sidechain) atom.

That said, it still can be useful to have these tree types be fixed,
especially if there is some consistency across families of residues.

> 2)Since the antechamber has assigned the tree name, why does the tleap not
> read and write directly from the parameter files? other than assign again?
> or let tleap assign the tree name and antechamber just ignores the tree
> question?

Antechamber didn't exist when leap was written, however there were
hand-written prep files with tree types in them. As far as I can
remember/conjecture at this point, the original author of leap decided
that the types served no purpose since they are not strictly chemical,
plus one must consider that leap introduced a dynamic molecule editor
which, insofar as it is used at all, means that tree types would need
to be recalculated on the fly. Also one must consider that without the
LOOP section, the tree types alone give an incomplete picture of the
bonds, which I believe is all they were originally intended for anyway.

In any case, when I took over leap I decided that at least main chain
types were useful, e.g. for TORSION BACKBONE in carnal, so I added an
on-the-fly calc of tree types to leap at prmtop-building time.

> 3) For a seperate ligand with limited number of atoms such 30, it is easy to
> check the tree name of ligand from the top file generated by tleap. and it
> seems ok if one doesnot put any constrains on the ligand. if it is not so,
> one has to be careful to check the selected atoms in the constrained group.
> 4)If the ligand is treated as an unusual residue in the middle of the whole
> structure, and if one wants to put on some constrains according to the group
> rules such as "* * S *", how about this situation?
> 5) if the tree type of "S" in parameter files becomes "E" by tleap, how
> about this change in the thereafter minimization or md simulations under
> constrained conditions?
> 6)I donot know whether there are something else to worry aoubt the tree name
> change.

You will have to think the ramifications through for yourself - I
think the only guaranteed use of tree types is for distinguishing
main chain atoms from the rest. Atom names and types may be your best
bet for group specification.


> From: Bill Ross <>
> Date: Sat Dec 30 2006 - 03:00:26 GMT
> >how does the tleap change the tree name after loading the PREP parameter
> >file?
> It discards the tree info and when doing saveamberparm it develops
> new tree types for each residue that has connect0 and connect1 atoms
> designated. The only really predictable thing about the new types is
> that the 'M' (main chain) atoms are on a shortest path between connect0
> and connect1.
> Bill
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Received on Wed Jan 03 2007 - 06:07:34 PST
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