Number of contacts between a protein or domain core and water molecules

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Deepshikha Ghosh 19310001

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Aug 24, 2022, 6:58:18 AMAug 24
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Hello MDanalysis Users

I wanted to calculate Q (Number of contacts between a group of residues in a core and water molecules) from the psf and dcd file. Is there any way out using MD analysis? Kindly suggest me.
Any sort of help will be appreciated.

Thanking You

Regards
Deepshikha Ghosh
IIT Gandhinagar

Oliver Beckstein

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Aug 24, 2022, 7:02:55 PMAug 24
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Hello Deepshika Ghosh,

On Aug 24, 2022, at 5:58 AM, Deepshikha Ghosh 19310001 <deepshik...@iitgn.ac.in> wrote:

Hello MDanalysis Users

I wanted to calculate Q (Number of contacts between a group of residues in a core and water molecules) from the psf and dcd file. Is there any way out using MD analysis? Kindly suggest me.

I don’t think we have a ready-made analysis tool for this purpose.

You should be able to use distance_array or capped_distance to calculate the distances between the solvent molecules and your protein.

A while back Alia implemented a simple solvation counter in MDPOW — you can look at the code  https://github.com/Becksteinlab/MDPOW/blob/2092cfd3f1cb006b38d01ec722dd2040f221a5c4/mdpow/analysis/solvation.py#L67-L75 ; Orion has a whole package dedicated to solvation-analysis https://github.com/MDAnalysis/solvation-analysis where you might also find inspiration. 

Maybe we did something like this in one of our workshop materials — perhaps someone else will chime in.

But I think you’ll have to write your own code.

Oliver

Any sort of help will be appreciated.

Thanking You

Regards
Deepshikha Ghosh
IIT Gandhinagar

--
Oliver Beckstein (he/his/him)

GitHub: @orbeckst

MDAnalysis – a NumFOCUS fiscally sponsored project





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