DL-FIND error with hdlc

3 posts / 0 new
Last post
asoyemi
DL-FIND error with hdlc

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')

khalilian
How to define residue list for hdlc

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.

tomkeal
tomkeal's picture
How to define residue list for hdlc

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

Log in or register to post comments