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

From: xiaoqin huang <>
Date: Tue, 02 Jan 2007 21:41:13 -0500

Well, It means that tleap only keep two ends of the molecule from parameter
files and assign again tree types to other atoms according to tleap's rules.

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

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

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.


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Received on Wed Jan 03 2007 - 06:07:33 PST
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