Wednesday, May 25, 2016

Automating calculations: pKa predictions

I want to compute the standard free energy difference for proton exchange between heliotridane and a molecule which I'll call compound 1 (comp1)

heliotridaneH+ + comp1 <=> heliotridane + comp1H+

To do this I need to geometry optimize in the gas phase and then do a single point calculation using a solvation model, all using GAMESS. I want to automate this so I can do it for comp2, comp3, ...

To do this I use bash and the python programs listed below

Step 1 make a file file called smiles.list which contains the name and SMILES strings, which defines both the molecule, the protonation state, and the conformation around the protonated N. I still need to automate this step.

Step 2  make so-called header files for the geometry optimization (pm6_opt.header) and solvation energy (pm6_sol.header) calculations.  These files contain the relevant keywords for the calculations.

Step 3 convert the SMILES strings to 3D coordinates (xyz files).

python smiles2coord.py smiles.list

This also creates som sdf files which I can now remove (rm *.sdf).


Step 4 convert the xyz files to GAMESS input files for geometry optimization
When naming the molecules in smiles.list I was carefull to label all the protonated forms with a "+".

for x in *.xyz; do babel -ixyz $x -ogamin ${x%.*}_opt.inp -xf pm6_opt.header; done

I could have modified smiles2coord_lis.py to generate these files directly, but I like to keep things modular.  At this point I can also get rid of the xyz files (xyz files).

Step 5 change the charge for the protonated forms.

sed -i 's/icharg=0/icharg=1/g' *+*.inp


Step 6 submit the GAMESS calculations.

for x in *_opt.inp; do submit_gamess $x; done

My GAMESS submit script is called "submit_gamess"

Step 7 wait til all the optimizations are done and that they all converged.

grep EQUILIBRIUM *.log

Step 8 transfer the optimized geometry to a new input file for the solvation energy calculations

for x in *_opt.log; do babel -igamout $x -ogamin ${x%.*}_sol.inp -xf pm6_sol.header; done

Step 9 change the charge for the protonated forms.

sed -i 's/icharg=0/icharg=1/g' *+*_sol.inp

Step 10 submit the GAMESS calculations.

for x in *_sol.inp; do submit_gamess $x; done

Step 11 wait til all the optimizations are done and that the calculations finished normally.

grep NORMALLY *_sol.log

Step 12 extract the last heat of formation in each file and put them in a file called energies

python readv2.py *._sol.log > energies

Step 13 find the lowest energy for each conformer and compute the relative energies and pKa values
python pka.py energies

Files referred to above





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