PCFF Error: core/script/build/system.c:251 ScriptBuildSystem: No mass in system 'main'

I’m trying to generate the PCFF parameters for the praziquantel molecule (https://atb.uq.edu.au/molecule.py?molid=573670) using EMC.
I am applying the following chemical.esh script:

#!/usr/bin/env emc_setup.pl


replace true
field pcff
field_increment ignore
number false
focus true
ntotal 1
density 0.1
emc_execute true



molecule O=C(N1CC(=O)N2C@@Hc1ccccc1CC2)C1CCCCC1,1


I am getting the following error

Info: types = {cff → {pair → {active → true, mode → repulsive}}}
Error: core/script/build/system.c:251 ScriptBuildSystem:
No mass in system ‘main’.
Program aborted.

Could anyone help me?

Hi Gabriela,

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):

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

# name			SMILES, number | mole fraction | mass fraction
molecule		O=C(N1CC(=O)N2C@@Hc1ccccc1CC2)C1CCCCC1, 1

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.

Thank you!