Frequently Asked Questions

Q. What is the recommended level of theory and basis set for generating various QM target data?

Ans: Recommended QM level of theory and basis set used for generating various different target data for additive and Drude parametrization

../images/qmlotbasis.png

Q. I am using stream file obtained from CGenFF, but file parsing is not complete. Why?

Ans: Check if you have more than one residues with same name in the stream file. Multiple residues with same residue names are not acceptable.

Q. I could not extract molecular polarizability from resname_opt.log. Why?

Ans: You need to run a single point QM calculation on optimized geometry with POLAR keyword at MP2/cc-pvQZ. Do not forget to remove OPT keyword if you are using Geometry Optimization tab to create this file..

Q. I supply everything as specified for MM calculation, but I could not run it successfully. Why?

Ans: Check the resname_mp2.crd for its correctness. It is possible that you extracted coordinates from a QM output file containing non-geometric target data (Containing water interaction or potential energy scan). This rewrites resname_mp2.crd. To correct this, load QM output file containing optimized coordinates in ExtractQMResults tab and re-extract the coordinates.

Q. When I create qm input files for Psi4, no _xyz.py file is created? What do I do?

Ans: Its a rdkit-numpy compatibility issue. First remove rdkit and numpy from ffpenv conda enviornment. Reinstall RDKit as: $conda install -c conda-forge rdkit. If numpy is getting installed as a dependency, its ok. Else install numpy separately.

Q. I get several repeated parameter errors during MM calculation of drude format stream file. How can I correct them?

Ans: This may be ignored by setting bomlev -1 in ffparam.inp before it reads resi.str.

Q. I get several missing parameter errors during MM calculation of drude format stream file. How can I correct them?

Ans: Copy those missing parameters in residue.str and manually assign parameters using parameter file in toppar_drude directory on the basis of closest match with the missing parameters in question.

Q. Nothing happens when I try to run MCSA calculation for charge alpha and thole. Why?

Ans: First of all increase the verbosity to 1 before running the calculation. This will print the whole command on terminal. Copy and paste this command on another terminal to check if you can find the source of the problem. Problem may be related to wrong format in residue.str file, qm_dipol.txt, qm_watint.txt or dafile.