Re: AMBER: leap saveamberparm chain types response

From: Bill Ross <>
Date: Thu, 17 Feb 2005 17:15:20 -0800 (PST)

> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -

The 'chain types' are seen in the old 'prep' format files.
They are basically a stack-based programming convention
used in indicating/calculating connectivity. Briefly and
somewhat accurately:

  M = main chain
  B = branch

If one has seen a branch atom when parsing sequentially, this
indicates that atom has a bond waiting to be satisfied by a later
atom. This convention gives a tree representation of the bonding
in a residue. The rings are closed by the LOOP section at the
end of the residue. Typically several different trees can be
formed on a residue (each with a different set of LOOP closures
if there are any rings). Some of these branch types can be
useful in selecting atoms for analyzing structure and energy,
e.g. the main chain can correspond to the backbone of a nucleic
acid and thus can be used to generate all the torsions without
tedious specification, such as in carnal's TORSION BACKBONE.

Leap doesn't keep track of tree types, e.g. since they would be
tedious to figure and label if creating a new residue interactively.
Since I had written carnal to use them, I wanted them in leap-
generated prmtops, and added a dynamic calc of them in the
saveparm commands. The minimal requirement is that connect0/connect1
atoms must be specified so that a breadth-first tree search can
find the shortest path between these atoms, which becomes the
main-chain atoms.

If connect0/connect1 are not specified, you just get the warning,
which has no effect unless you use carnal or the chain part of the
GROUP spec in sander etc.

Since carnal is on its way out of amber, perhaps the whole chain
thing could be dropped from the leap code, since I doubt that
anyone uses it in sander.


> In leap, the saveamberparm unit name.prmtop name.inpcrd results in
> the following response.
> Not Marking per-residue atom chain types.
> Marking per-residue atom chain types.
> (Residues lacking connect0/connect1 -
> these don't have chain types marked:
> res total affected
> SCH 95
> )
> (no restraints)
> What exactly does this mean? What does the 'residues lacking
> connect0/connect1' mean? What does the chain types marked mean?
> Or do you know where in the docs to find an explanation?
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Received on Fri Feb 18 2005 - 01:53:00 PST
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