Multiwfn forum

Dobelman

Member

Registered: 2022-02-18

Posts: 5

Batch calculate MPP planarity index

I'm using 3.8 dev version to calculate MPP.
once the file is uploaded I press
- MPP
- a (or all atoms)
Then MPP and SDP are calculated.

I tried to use in analogy to the examples for the genELFcub.txt
the following sequence
MPP
a
2

So far I did not succedd to do this in batch mode from .xyz or .mol files.

also when using the 3.7 version it crashes afte adding MMP.

Thanks for helping me out!
Dobelman

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Batch calculate MPP planarity index

Dear Dobelman,

In batch model, which file was used as input file? Note that the input file must contain geometry information, otherwise MPP cannot be calculated.

MPP was proposed last year, while Multiwfn 3.7 was released in 2020, thus Multiwfn 3.7 doesn't support MPP. Please always use latest version of Multiwfn. Multiwfn updates quite frequently.

Best regards,

Tian

Dobelman

Member

Registered: 2022-02-18

Posts: 5

Re: Batch calculate MPP planarity index

Dear Tian,

as input file I use 3D files like .xyz or .mol.
In command line it works fine, but I cannot get it working in batch mode.

Can you help or maybe post an example?

Thank you very much for your help!
Dobelman

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Batch calculate MPP planarity index

Dear Dobelman,

This is an example of shell script. The script loops over all .pqr file and calculate MPP for them.

#!/bin/bash
for filename in `ls *.pqr`
do
echo calculating $filename ...
echo -e "MPP\na\nn\nq" | Multiwfn $filename | grep "Molecular planarity parameter (MPP)"
done

Result:

calculating 10.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.540130 Angstrom
calculating 12.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.555101 Angstrom
calculating 14.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.334641 Angstrom
calculating 16.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.346409 Angstrom
calculating 18.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.119724 Angstrom
calculating 20.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.334525 Angstrom
calculating 22.pqr ...                                      
 Molecular planarity parameter (MPP) is    0.200972 Angstrom
calculating 4.pqr ...                                       
 Molecular planarity parameter (MPP) is    0.000000 Angstrom
calculating 6.pqr ...                                       
 Molecular planarity parameter (MPP) is    0.000000 Angstrom
calculating 8.pqr ...                                       
 Molecular planarity parameter (MPP) is    0.728097 Angstrom

Best,

Tian

Dobelman

Member

Registered: 2022-02-18

Posts: 5

Re: Batch calculate MPP planarity index

Hi Tian,

I'm forced to use Windows. Can you also help here, please?

Thank you!
Dobelman

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Batch calculate MPP planarity index

Hi Tian,

I'm forced to use Windows. Can you also help here, please?

Thank you!
Dobelman

You can use "cmder"  to simulate Bash environment under Windows, then you can use Bash shell script as Linux. It is quite convenience.

Screenshot:

Dobelman

Member

Registered: 2022-02-18

Posts: 5

Re: Batch calculate MPP planarity index

Hi Tian,

so I used cmder, but now I need to point to the exe file.
I have all files in same folder, but still I'm not able to find the executable.
What do I miss?

Kind regards,
Dobelman

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,830

Website

Re: Batch calculate MPP planarity index

Dear Dobelman,

You need to add the folder containing Multiwfn.exe to "Path" environment variable of your Windows system, you can easily find how to do using Google. Alternatively, you should write absolute path of Multiwfn.exe so that it can be found.

Best regards,

Tian

Dobelman

Member

Registered: 2022-02-18

Posts: 5

Re: Batch calculate MPP planarity index

Hi Tian,

thank you for your help!

This work well now :-)

Best,
Dobelman