Hi,
I was trying to do a QM/MM calculation using HDLC but I got the following error in the output file
DL-FIND ERROR:
No residues present in dfl_hdlc_init
Below is my input file
from chemsh import *
from chemsh.cluster.getFrozen import getNotQM
# Creation of mfi cluster fragment
mfi = Fragment(coords='cupc2.pun', connect_mode='covalent')
ff = 'zeolite_gulp.ff'
# Parameters of the qmmm object
qm_theory = ORCA(method='dft', functional="b3lyp", basis="def2-svp", scftype='uks',mult=2, optstr='!D3BJ def2/J RIJCOSX ',path="/share/apps/orca/orca_5_0_2_linux_x86-64_shared_openmpi411/orca",nprocs=16)
mm_theory = GULP(ff=ff,conjugate=True)
#get active region which will be optimized
active_region = mfi.getRegion(1,3)
qm_region = mfi.getRegion(1)
# Parameters of boundary_charge_adjust function in qmmm.py file
silicate_modifiers = {("Si","o1"):0.3}
reverse_silicate_modifiers = {("Si","o1"):-0.3}
# Creation of qmmm object
qmmm = QMMM(qm=qm_theory,
mm=mm_theory,
frag=mfi,
coupling='covalent',
qm_region=qm_region,
embedding='electrostatic',
dipole_adjust=True)
# Using a looser than usual tolerance to ensure quick convergence
opt = Opt(theory=qmmm,
algorithm="lbfgs", coordinates='hdlc', tolerance=0.0045, trust_radius="energy",
maxcycle=500, maxene=500, active=active_region,save_path=True)
opt.run()
# Saving of optimized cluster
mfi.save('cupc2_opt.pun', 'pun')
mfi.save('cupc2_opt.xyz', 'xyz')
I am having the same issue. I know that for using "hdlc" coordinates, list of residues should be defined and this error is because you have not defined the residue list. However I do not know how the list of residues can be defined in py-Chemshell. If anyone could help with this that would be great.
Hi both,
Apologies for this, at present the HDLC residues definition is not exposed in the Py-ChemShell interface to DL-FIND. This will definitely be fixed in the next release of Py-ChemShell.
Best wishes,
Tom