Re: AMBER: residues and molecules

From: David A. Case <>
Date: Wed, 24 Sep 2003 11:45:40 -0700

On Tue, Sep 23, 2003, GUILLERMINA L ESTIU wrote:
> The problem is that (I don't know how) tleap properly build the residues, but
> messes up the definition of the molecules : a molecule ends in the middle of a
> residue.

What variables are you looking at to decide where the molecules begin and end?
I think sander only cares about this for determining the pressure, and that
the differences between different "molecule" definitions probably have
a negligable effect, as long as the waters are correctly identified (they
dominate by far the pressure calcualtion).

I can't tell from your e-mail what could have gone wrong -- you mention
something about a "unit docked", but I did not understand that. Generally,
the input pdb file to LEaP needs to have a TER card at the end of every's not clear to me whether or not that was the case for your

Of course, there could be glitches in the way LEaP figures out molecules, but
one would need more information to delve into this.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Sep 24 2003 - 19:53:01 PDT
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