ok, thanks for your reply, I feel better.
>From: Bill Ross <ross.cgl.ucsf.edu>
>Reply-To: amber.scripps.edu
>To: amber.scripps.edu
>Subject: Re: AMBER: Re:tree name generated by tleap is different from the
>input PREP parameter file
>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.
>
>Bill
>
> >
> >
> >
> > From: Bill Ross <ross.cgl.ucsf.edu>
> > 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 Sun Jan 07 2007 - 06:07:08 PST
