AMBER Archive (2003)

Subject: Re: AMBER: residues and molecules

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 24 2003 - 13:45:40 CDT

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
molecule...it's not clear to me whether or not that was the case for your
example.

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

..dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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