Section Content
1 Preparation
2 XTB
3 Running

Prep

  1. This guide will serve to help you do XTB calculations linked to Gaussian software.
  2. A script (xtb.sh) and two executables (genxyz and extderi) must be downloaded from gau_xtb. The code is written by Dr Tian Lu. He has made many other interesting computational chemistry programs too.
  3. The gau_xtb.zip file can be unzipped and transferred into Gadi. Remember to chmod +x files in order to make the executable files work.
  4. Next download the precompiled version of XTB and transfer the compressed file into Gadi.
  5. After tar xf xtb-200917.tar.xz to extract the tarball you will find that it should contain bin and share - if it doesn’t you have downloaded the source files which you will need to compile yourself.
  6. In home /~ directory nano .bashrc and add these lines: 
    export PATH=$PATH:~/xtb-6.3.3/bin
export XTBPATH=~/xtb-6.3.3/share/xtb
export OMP_NUM_THREADS=4
export MKL_NUM_THREADS=4
export OMP_STACKSIZE=1000m
ulimit -s unlimited
  7. Exit and . .bashrc

XTB

  1. The calculations will use the parameter which is GFN2-xtb. This is a semi-empirical tight binding model which means it will take into account non-covalent interactions and is up a level from semi-empirical methods like PM6.
  2. Read more about the method here
  3. Since GFN2 is considered a semi-empirical qc method, it should be applicable to calculating large molecules like small proteins as the computational cost is lower than DFT methods like B3LYP.
  4. You can consider using this method to calculate and locate minimum of transition state structures first. It will give a good guess of the electronic structure before optimizing further with DFT. It is linked by gau_xtb program with Gaussian.

Running

  1. The script xtb.sh, and executable files extderi and genxyz have to be in the working folder.
  2. In the keywords route the input gjf should have external='./xtb.sh' included. If frequency job is required, use the gaussian link1 keyword. A typical optimization job:
%chk=mol.chk
%nprocshared=4
%mem=8GB
#p opt=nomicro external='./xtb.sh'

Mol opt by gfn2-xtb

0 1
 (xyz cartesian)

--link1--
%chk=mol.chk
%nprocshared=4
%mem=8GB
#p freq external='./xtb.sh' geom=allcheck
<blank space>
  1. For TS and PES, change opt=nomicro to opt=(ts,calcfc,noeigen,nomicro) or opt=(modredundant,maxcyc=20,nomicro).