Current version of ffmaker produces force field files using gaussian and antechamber. Subsequently, this script should be run on Hyak. An ffmaker version using opensource tools may be in the future. for now the following must be in the path:
g09root=/gscratch/pfaendtner/codes/G09
AMBERHOME=/gscratch/pfaendtner/vjaeger/software/amber11b
you will need to edit ffmaker.inp to reflect the molecule you are parameterizing (and make any additional changes suited for your needs):
###ALL COMMANDS ARE CASE SENSITIVE. SEE EXAMPLES###
###STANDARD INPUTS###
RESIDUE_NAME=TF2 #three characters, letters should be caps. example: BMI, 1EM, P00
INPUT_TYPE=pdb #com (recommended), pdb (also a good choice), mol2
CHARGE=-1 #1,-1, or 0 usually
SCALED=yes #Do you want to scale the charges? (yes, no)
FACTOR=0.8 #Scaling factor.
###CONDITIONAL INPUTS###
REPLACE_HF=no #You can replace hartee fock with a different method. no (default), b3lyp, mp2
#REPLACE_631=no #You can replace 6-31G* with a different basis set. no (default), 3-21G, 6-311G*. not currently working.
METHOD=resp #resp (recommended), esp, bcc
G09_MEM="%mem=1000MB" #Gaussian memory
G09_PROC="%nproc=16" #Gaussian processors
REPLACE_FF=no #Change force field to something other than amber99sb-ildn. no (default), ff99sb
As stated in INPUT_TYPE you will need to provide a pdb or com file of your molecule.
guassian/antechamber typically run fine on an interactive node (do not run on the login nodes):
source ffmaker.bash