1. openCOSMO-RS_conformer_pipeline 📏#
The openCOSMO-RS_conformer_pipeline program is essential for the generation of the input files containing all necessary information about the molecules structure. Furthermore this program needs:
ORCA 6.0++
xtb executables
Balloon (optional, but for certain molecule predictions is necessary)
1.1. Requirements to install 🔧#
1.1.1 ORCA 6.0.1 🐋#
ORCA is a computational chemistry tool package used for quantum chemistry calculations. It is indispensable to generate the input files containing the molecule’s chemical information and its properties.
Create an account in the ORCA website
Go to downloads and install ORCA 6.0++
Run the installation and choose the full version of orca, the basic one will not work.
The Orca installation folder needs to be added to the path variables in the system environment. For windows, in the search bar type “system environment” and click on the option that appears called Edit the system environment variables.
You should see a section below called System Variables. Find the row that is called Path, click on edit and add the ORCA path, like so: “C:\ORCA_6.0.1”
For steps 4 and 5 we can also use python:
import os
import subprocess
# 1. Define the ORCA installation path
orca_path = r"C:\ORCA_6.0.1"
# 2. Get the current PATH environment variable - this is analogue to looking up the system environment option and selecting the "path" variable
current_path = os.environ['PATH']
# 3. Check if the ORCA path is already in the PATH, if not it will add it
if orca_path not in current_path:
# Add the ORCA path to the PATH
new_path = f"{current_path};{orca_path}"
# Use setx command to permanently set the PATH variable
subprocess.run(['setx', 'PATH', new_path], shell=True)
print(f"ORCA path added to PATH: {orca_path}")
else:
print("ORCA path is already in the PATH.")
ORCA path is already in the PATH.
# We can verify if the ORCA installation is correct by running the following command
# remember to change the path name "ORCA_6.0.1" to the one you setted up before
!C:\ORCA_6.0.1\orca --version
*****************
* O R C A *
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#########################################################
# -***- #
# Department of theory and spectroscopy #
# #
# Frank Neese #
# #
# Directorship, Architecture, Infrastructure #
# SHARK, DRIVERS #
# Core code/Algorithms in most modules #
# #
# Max Planck Institute fuer Kohlenforschung #
# Kaiser Wilhelm Platz 1 #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#########################################################
Program Version 6.0.1 - RELEASE -
With contributions from (in alphabetic order):
[Max-Planck-Institut fuer Kohlenforschung]
Daniel Aravena : Magnetic Suceptibility
Michael Atanasov : Ab Initio Ligand Field Theory (pilot matlab implementation)
Alexander A. Auer : GIAO ZORA, VPT2 properties, NMR spectrum
Ute Becker : All parallelization in ORCA, NUMFREQ, NUMCALC
Giovanni Bistoni : ED, misc. LED, open-shell LED, HFLD
Martin Brehm : Molecular dynamics
Dmytro Bykov : pre 5.0 version of the SCF Hessian
Marcos Casanova-Páez : Triplet and SCS-CIS(D). UHF-(DLPNO)-IP/EA/STEOM-CCSD. UHF-CVS-IP/STEOM-CCSD
Vijay G. Chilkuri : MRCI spin determinant printing, contributions to CSF-ICE
Pauline Colinet : FMM embedding
Dipayan Datta : RHF DLPNO-CCSD density
Achintya Kumar Dutta : EOM-CC, STEOM-CC
Nicolas Foglia : Exact transition moments, OPA infrastructure, MCD improvements
Dmitry Ganyushin : Spin-Orbit,Spin-Spin,Magnetic field MRCI
Miquel Garcia-Rates : C-PCM and meta-GGA Hessian, CCSD/C-PCM, Gaussian charge scheme
Tiago L. C. Gouveia : GS-ROHF, GS-ROCIS
Yang Guo : DLPNO-NEVPT2, F12-NEVPT2, CIM, IAO-localization
Andreas Hansen : Spin unrestricted coupled pair/coupled cluster methods
Ingolf Harden : AUTO-CI MPn and infrastructure
Benjamin Helmich-Paris : MC-RPA, TRAH-(SCF,CASSCF), AVAS, COSX integrals, SCF dyn. polar.
Lee Huntington : MR-EOM, pCC
Robert Izsak : Overlap fitted RIJCOSX, COSX-SCS-MP3, EOM
Riya Kayal : Wick's Theorem for AUTO-CI, AUTO-CI UHF-CCSDT
Emily Kempfer : AUTO-CI, RHF CISDT and CCSDT
Christian Kollmar : KDIIS, OOCD, Brueckner-CCSD(T), CCSD density, CASPT2, CASPT2-K, improved NEVPT2
Axel Koslowski : Symmetry handling
Simone Kossmann : meta-GGA functionals, TD-DFT gradient, OOMP2, (MP2 Hessian; deprecated post 5.0)
Lucas Lang : DCDCAS
Marvin Lechner : AUTO-CI (C++ implementation), FIC-MRCC
Spencer Leger : CASSCF response
Dagmar Lenk : GEPOL surface, SMD, ORCA-2-JSON
Dimitrios Liakos : Extrapolation schemes; Compound Job, initial MDCI parallelization
Dimitrios Manganas : Further ROCIS development; embedding schemes. LFT, Crystal Embedding
Dimitrios Pantazis : SARC Basis sets
Anastasios Papadopoulos: AUTO-CI, single reference methods and gradients
Taras Petrenko : pre 6.0 DFT Hessian and TD-DFT gradient, (ASA, deprecated), ECA, 1-Electron XAS/XES, NRVS
Peter Pinski : DLPNO-MP2, DLPNO-MP2 Gradient
Christoph Reimann : Effective Core Potentials
Marius Retegan : Local ZFS, SOC
Christoph Riplinger : Optimizer, TS searches, QM/MM, DLPNO-CCSD(T), (RO)-DLPNO pert. Triples
Michael Roemelt : Original ROCIS implementation
Masaaki Saitow : Open-shell DLPNO-CCSD energy and density
Barbara Sandhoefer : DKH picture change effects
Kantharuban Sivalingam : CASSCF convergence/infrastructure, NEVPT2 and variants, FIC-MRCI
Bernardo de Souza : ESD, SOC TD-DFT
Georgi L. Stoychev : AutoAux, RI-MP2 NMR, DLPNO-MP2 response, X2C
Van Anh Tran : RI-MP2 g-tensors
Willem Van den Heuvel : Paramagnetic NMR
Zikuan Wang : NOTCH, Electric field optimization
Frank Wennmohs : Technical directorship and infrastructure
Hang Xu : AUTO-CI-Response properties
[FACCTs GmbH]
Markus Bursch, Miquel Garcia-Rates, Christoph Riplinger, Bernardo de Souza, Georgi L. Stoychev
APM, Basis sets (HGBS, AHGBS, def-TZVP (Ac-Lr), def2-XVPD (La-Lu)), CI-OPT, improved COSX, DLPNO-Multilevel,
DOCKER, DRACO, updates on ESD, GOAT, IRC, LR-CPCM, MBIS, meta-GGA TD-DFT gradient, ML-optimized integration grids,
MM, NACMEs, nearIR, NEB, NEB-TS, NL-DFT gradient (VV10), 2- and 3-layer-ONIOM, interface openCOSMO-RS, QMMM,
Crystal-QMMM, SF, symmetry and pop. for TD-DFT, r2SCAN hybrids, SOLVATOR
[Other institutions]
V. Asgeirsson : NEB
Christoph Bannwarth : sTDA-DFT, sTD-DFT, PBEh-3c, B97-3c, D3
Sebastian Ehlert : rSCAN, r2SCAN, r2SCAN-3c, D4, dhf basis sets
Marvin Friede : D4 for Fr, Ra, Ac-Lr
Lars Goerigk : TD-DFT with DH, B97 family of functionals
Stefan Grimme : VdW corrections, initial TS optimization, DFT functionals, gCP, sTDA/sTD-DF
Waldemar Hujo : DFT-NL
H. Jonsson : NEB
Holger Kruse : gCP
Marcel Mueller : wB97X-3c, vDZP basis set
Hagen Neugebauer : wr2SCAN
Tobias Risthaus : range-separated hybrid DFT
Lukas Wittmann : regularized MP2, r2SCAN double-hybrids, wr2SCAN
We gratefully acknowledge several colleagues who have allowed us to
interface, adapt or use parts of their codes:
Ed Valeev, F. Pavosevic, A. Kumar : LibInt (2-el integral package), F12 methods
Garnet Chan, S. Sharma, J. Yang, R. Olivares : DMRG
Ulf Ekstrom : XCFun DFT Library
Mihaly Kallay : mrcc (arbitrary order and MRCC methods)
Frank Weinhold : gennbo (NPA and NBO analysis)
Simon Mueller : openCOSMO-RS
Christopher J. Cramer and Donald G. Truhlar : smd solvation model
S Lehtola, MJT Oliveira, MAL Marques : LibXC Library
Liviu Ungur et al : ANISO software
Your calculation uses the libint2 library for the computation of 2-el integrals
For citations please refer to: http://libint.valeyev.net
Your ORCA version has been built with support for libXC version: 6.2.2
For citations please refer to: https://libxc.gitlab.io
This ORCA versions uses:
CBLAS interface : Fast vector & matrix operations
LAPACKE interface : Fast linear algebra routines
Shared memory : Shared parallel matrices
[file orca_main/run.cpp, line 380]: Cannot open input file: --version
[file orca_main/run.cpp, line 380]: Cannot open input file: --version
1.1.2 xtb executables 📄📄#
It is necessary to download the xtb 6.7.1 for the current version of ORCA (6.0.1)
Download the program
Go to the “bin” folder and you will see two files: xtb and libiomp5md.dll
Rename the xtb to otool_xtb
Go to the ORCA directory (it is located path that you setted up before, in this example is: “C:\ORCA_6.0.1” .
In this directory you should see a bunch of files beginning with orca_2…Drag the two previous files mentioned to the ORCA directory
1.1.3 Balloon 🎈#
It is optional to download, but we can use this program as well as RDKit to generate the starting conformers. In case RDKit fails, we have this program as a backup
The steps to follow are similar to what we did for the xtb executables:
Download the program here
Unzip the file and you will see two “Multi-File Format” or mff files: balloon and MMFF94.mff
Drag both into the ORCA folder that we setted up before, in here you should see the ORCA files as well as the otool_xtb files!