HTML Basics
Basic Tags
NAME
The NAME attribute allows you to mark certain points of a document
as places that can be jumped to directly. This is done using the
form <A NAME="label">...</A> where
label is any text you choose. The format of the Link tag
now becomes:
<A HREF="http://www.presidents.com/names.htm#clinton">Clinton</A>
or
<A HREF="#clinton">Clinton</A>
with the linked file (www.presidents.com/names.htm) having the
following format:
<A NAME="clinton">Clinton, Bill</A> is the president of the US.
This enables you to build an index at the top of a long document and jump to linked text within
it.
For example, try jumping to the end of this document.
Start of very boring document
In Stage 1 we generate alpha-helices with good stereochemistry and good van der Waals
interactions. However, we neglect electrostatic interactions in this first stage. Also, during Stage 1,
the C-alpha atoms remain fixed throughout to serve as a template on which helix generation could
occur. Stage 2 will address both these points. Stage 2 involves a brief cooling of 4 ps from 500 to
300K during which the C-alpha atoms are gradually freed from initial restraints. During this phase
we switch on the electrostatic energy term. Electrostatic interactions between polar and charged
sidechains are gradually introduced by scaling the partial atomic charges of sidechain atoms.
Then we perform a short (5 ps) constant temperature (300 K) MD refinement with the C-alpha
atoms free from restraints. Repeat runs of Stage 2 with structures generated from Stage 1 produces
a final ensemble of structures.
During Stage 2 we apply a number of distance restraints to the structure. Biharmonic distance
restraints are applied between the carbonyl oxygen of residue i and the amide hydrogen of residue
i+4 . The target distance for these restraints are derived from analysis of hydrogen bonding
distances in protein alpha-helices. Additionally, when generating alpha-helix bundles we applied
inter-helix distance restraints. These latter restraints had a one-sided harmonic function such that the
energy penalty was only active if the inter-helix distance exceeded 11.5 Angstroms. Thus close
packing of helices was not prevented by these restraints.
At last, the end is in sight Did you realise that Molecular Dynamics was so interesting?
By using a <A href="#end">end</A> link at the top of this document you can jump to the corresponding <A name="end"> at the end of the document.
Check the source if you like.
Agenda
HTM140