Hi,
I find some information here :
http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/htmlman.html
And for a more usefull answer, they explain that :
The hbuild statement tries to build the position of any selected
hydrogen based on the position of the heavy atom antecedents (Brünger
and Karplus 1988). It works in a general way and can be used with any
empirical force field. It performs local energy minimization in cases
where the placement of the hydrogens is not unique. Waters close to the
macromolecule are placed first, followed by waters that are farther
away. Several iterations can be carried out to reach self-consistency.
The minimization uses the energy function (Eq. 4.1
<http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node113.html#eqetotal>)
except that the specification of constraints interaction statements
(Section 4.7
<http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node131.html#constraintsinteraction>)
are ignored.
The hydrogen building facility does not use the improper or dihedral
information in the topology file (Section 3.1.1
<http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node46.html#topologystatement>).
The chirality of methyl and methylene groups is determined by the order
of four substituents to the central carbon atom as specified in the
molecular structure. By changing the order in which the atoms are
defined in the residue statement (Section 3.1.1
<http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node46.html#topologystatement>),
the chirality of the center is changed.
Hydrogens are recognized by X-PLOR by their mass. All atoms with a mass
less than 3.5 amu are considered hydrogens. Certain simulated annealing
protocols (e.g., Section 20.3.3
<http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node395.html#dgsaprotocol>)
make use of artifically increased masses. If hydrogen building is
employed in these protocols, the hydrogen building routine will return
an error statement. In this case the user has to reset the mass of the
hydrogen atoms to their physical values.
To save CPU time, it is suggested to carry out the hydrogen building
without nonbonded energy terms. The coordinates then will need
minimization to relieve possible bad contacts between the initial
hydrogen placements.
You can find more information about the CHARMM force field apllied to
the Explicit polar hydrogens of Nucleics acids and proteins
HTH
Nicolas
Le 27/04/12 15:34, Nadir T. Mrabet a écrit :
Hi,
Could someone explain to me the scientific details of the protocols
used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray
structures and (2) optimize their positions?
Many thanks in advance.
Greetings,
Nadir
