Biomedical Engineering Reference
In-Depth Information
17
HF-LCAO Examples
I am going to start with l-phenylanine, as in Chapters 4-6, to exemplify the principles
discussed so far for the HF-LCAOmodel. There are a number of commercial packages that
perform (amongst other things) HF-LCAO calculations, and everyone has their favourites.
All the packages will do the simplest types of application whilst certain algorithms are only
found in a subset of the available packages.
I am going to use mostly Gaussian 03 (http://www.gaussian.com) from this point on, but
I stress that it is to a large extent a matter of personal choice and what is available on your
local computer facilities.
The simplest way for me to run a job on my local Unix system, given that I already have
Protein Data Bank (.pdb) files from earlier chapters, is to edit a .pdb file to produce a 'Gaus-
sian job file' (these have extensions .gjf) and run the job. In a typical Unix environment I
might type (after the $ prompt)
-bash-3.00$ module load gaussian
-bash-3.00$ g03 <phenylanine.gjf >phenylanine.out
A suitable .gjf file is given below.
%chk=phenylanine.chk
# HF/6-311G** Pop=Full SCF=Direct
L-phenylanine
01
N
0.000 0.000
0.000
H
0.000 0.000
1.010
C
1.366 0.000 -0.483
