grimme-lab / crenso Goto Github PK

Hello!
I read the paper you all wrote on the CRENSO package, and I would like to be able to use CRENSO specifically for calculating pKa values on a number of small organics. After reviewing the code and help strings, I understand that a Turbomole coord file is needed in a directory when calling CRENSO, and I understand that when running pKa, the acid and base species must both be specified within a single coord file with corresponding charges (as noted here

for example).

Unfortunately I do not have the Turbomole package, and after browsing some of the Turbomole documentation, I am not sure how to place both the acid and base molecules within the a single coord file with the charges specified. Would it be possible to include an example coord file for, say, methanol and its conjugate base? I checked the supporting information for several papers that cite CRENSO, I have not seen an example input file that I can use as a template that works with CRENSO. If one could be placed in this package (or in the README.md), that would be super helpful.

Alternatively, would it be possible to have separate acid.xyz and base.xyz files that could be passed to CRENSO via flags? Thereby obviating the need to drop to a Turbomole coord format at all? I recognize that this might take some refactoring (places like here

for example), but I think this would be a very helpful improvement.

Thanks so much!

Hello grimme-lab,

I highly use and appreciate the programs and packages you developed and provide. Especially, the crenso and crest_combi scripts are useful.
However, recently I encountered an issue while using the l0 and l0opt keywords of crenso. The output (attached) furnished the following error during the censo part:

censo: error: argument -part1/--part1: invalid choice: '' (choose from 'on', 'off')

I also attached my submission script to rule out any mistakes there. Maybe it's due to some of my settings of crenso but as far as I understand crenso correctly invoking the single parts of censo is handled by the crenso script without further settings needed.

Thanks for the tools and your help.

error.zip

Hi
I have been using crest_combi on another cluster fine
now with a new one, were crest is working fine and placed on the bin directories
I am trying to run crest_combi
but I have that error
#>>># Running: CREST 1 (FF,-v4)
/storage/scratch/lv82/lv82834/bin/crest_combi: line 125: crest: command not found
etc...

(the exact same slurm bash without crest_combi but with crest works fine!!!)
the coord file is well added and the charge by its own as well

I dont understand
was there something else I forget to do
I did the chmod +x crest_combi so it is well in rwxr-xr-x mode all the other ones

crest_combi.zip

thank you for your help

On my side, lines 97 and 98 of the crest_combi script fail with the following error:
invalid arithmetic operator (error token is ".0")
Replacing them with the following lines solves this issue:

ewin2=$(echo "$ewin+4" | bc) # ewin for intermediate FF run re-ranking with GFN2
ewin3=$(echo "$ewin-2" | bc) # ewin for last GFN2 search (if mode="")

thank you for the very nice work

Shellcheck complains on quoting for crenso and crest_combi.

shellcheck crenso
shellcheck crest_combi

Might be worth investigating and setting up a linting workflow for this repository.