To create the lis-data files of the BPTI test dataset change to the
directory containing the X-PLOR data
cd $(HOME)/ego/testbpti/
and start the conversion utility program xpl2lis by typing
$(HOME)/ego/ALPHA/xpl2lis ../utils/units.def pti.pdb pti.psf param19.pro
This example works if you have compiled EGO via aimk for a DEC-ALPHA
computer.
During conversion some information on the newly created lis-files is given. Make shure that no warning errors occur during conversion and that xpl2lis does not stop with an fatal error. Each lis-file consists of a short header section which gives information on type and format of the included data. The file units.def located in the directory $(HOME)/ego/utils is a ASCII file and is needed for FAMUSAMM, which groups atoms into structural units in order to obtain rapidly converging multipole expansions. For every molecule structure (e.g., water, proteins, lipids, etc.) a corresponding subdevision into such structural units has to be given in the file units.def. In the units.def file of your EGO distribution such structural units are already defined for TIP3-water molecules, proteins and some lipids. If you intend to simulate molecules for which a proper subdevision into structural units is not already given, you first must edit the units.def file. A detailed description on this procedure is given in Sec. A.1.1.