CP/MM Tutorial

Copy the log file of Gaussian with the electrostatic grid information on a new directory
and use the following command: 9
antechamber -i electrostatic_grid.log -fi gout -c resp -nc 0 -m 1 -o
acetone.resp.prep -fo prepi -rn ACET
Actually, Antechamber recalls several programs in sequence that produce many
different intermediate files in your directory. When the process ends correctly you
should see the file acetone.resp.prep that is the file with the partial RESP charges that
we will use in the next step (copy it in a new directory and move to it).
5 – Water box
It is time to create the water box containing the acetone and the files necessary to run a
short classical Molecular Dynamics (MD) run. In fact, we want then to perform a
classical pre-equilibration of the system, in order to relax it near to a “stable state”. 10
For this aim we will use the Graphical User Interface Xleap of Amber11:
xleap -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB &
where the file leaprc.ff99SB is used to load all libraries which contains the parameters of
the Amber force field 99SB. Such a force field like any others has been tuned to
describe aminoacids, nucleic acids, etc but there is no information about acetone. For
this reason we have calculated the partial charges, which now we can load in Xleap by
typing the following command (in the Xleap main window): 11
loadamberprep acetone.resp.prep
and for the same reason some other parameters are still missing and have to be added
manually. Most of them can be retrieved by the “general Amber force field for organic
molecules GAFF”:
loadamberparams $AMBERHOME/dat/leap/parm/gaff.dat
other ones, however, have to provide manually. It is not difficult to calculate them but
here we will no explain how to do 12 . We have already prepared a file with such missing
parameters (above all bond and angles ones) and they can be load in Xleap by the
following command:
loadamberparams /home/ei250498/TUTORIALS/ACETONE/5-XLEAP/acetone.frcmod
You can now give a look at your system by the command edit:
9 Run simply the command “antechamber” to have a short description of the meaning of all the
option recognized by antechamber.
10 Remember the time step for a classical MD run is ~ps, while the time step for a quantum MD is
~fs. So, the classical pre-­‐equilibration is essential since typical relaxation times are of the order
of 10s-­‐100s of ps!
11 The syntax for any Xleap command can be recall by typing the command without any
arguments.
12 Refer to the Amber manual, for example.