Info: types = {cff → {pair → {active → true, mode → repulsive}}}
Error: core/script/build/system.c:251 ScriptBuildSystem:
No mass in system ‘main’.
Program aborted.
The error you are experiencing is generated by the build paragraph in your build.emc. EMC reports, that no atoms exist to be built. This results from your chosen settings under ITEM OPTIONS, i.e. you requested EMC to build one atom (ntotal 1) at a density of 0.1 g/cc (density 0.1) using mol fractions by default. Unfortunately, your praziquantel molecule has more than one atom. To remedy this you can either increase ntotal to the number of atoms in your molecule or set the number option to true (number true):
ITEM OPTIONS
replace true # replace already written input scripts
field pcff # choose PCFF as force field
field_increment ignore # ignore missing bond increments
number true # assume number of molecules
focus true # center built molecule in box
ntotal 1 # total number of built atoms
# ignored when number is set to true
density 0.1 # density in g/cc of built system
emc_execute true # execute EMC after generation of
# input scripts
ITEM END
ITEM SHORTHAND
# name SMILES, number | mole fraction | mass fraction
molecule O=C(N1CC(=O)N2C@@Hc1ccccc1CC2)C1CCCCC1, 1
ITEM END
The above will build exactly one praziquantel molecule with density 0.1 g/cc and place the center of mass of the resulting molecule at the center of your simulation box. Please note that the number after your SMILES refers to either the requested number, mole fraction, or mass fraction of molecules to be built. The is selected by setting either number true, mol true, or mass true respectively under ITEM OPTIONS. As mentioned, the default option is mol true.