pairwise rmsd calculation

Ali Raza

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Aug 20, 2021, 8:42:59 AM8/20/21

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hello dear,

i have calculated RMSD values for lig-pro complex and now am trying to calculate pairwise rmsd through MDAnalysis. i certainly unsure about the types of files to use for this calculation.

Thanks & Regards

ALI RAZA

Irfan Alibay

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Aug 20, 2021, 8:47:47 AM8/20/21

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Hi,

Welcome to MDAnalysis!

From the image you sent, I'm not sure what file formats you are using you build your Universe. It looks like you are passing a `xlsx` file for the trajectory? Could you give more details about what this file is?

Best regards,

Irfan

Ali Raza

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Aug 20, 2021, 9:04:57 AM8/20/21

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Dear Irfan,

Yes, i am using excel and pdb file while previously i used dat files ftom rmsd which don't work.

I want to know which files will work in Jupyter and how to prepare them as I've dat files from amber

Thanks and regards

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Irfan Alibay

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Aug 20, 2021, 9:24:21 AM8/20/21

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Hi,

I think you might have to give us more information about what you are trying to do. For example, what files do you have, and what are within those files? And also what is your end goal based on these inputs (i.e. do you already have all the RMSD values you need, or are you looking to calculate pairwise RMSD values?)

With regards to the error you're currently getting. The MDAnalysis.Universe object is constructed from a topology and a structure/trajectory file. In this case it seems like it's from an AMBER simulation, then you would likely want to pass your PRMTOP topology as your first file, and your netcdf trajectory as the second file.

I suggest having a look at our userguide for more information on how to use the MDAnalysis library: https://userguide.mdanalysis.org/stable/index.html

In the first instance, this section of the quick start guide would probably go into more details of how to build a Universe: https://userguide.mdanalysis.org/stable/examples/quickstart.html#Loading-a-structure-or-trajectory
This example on pairwise RMSD might be of interest: https://userguide.mdanalysis.org/stable/examples/analysis/alignment_and_rms/pairwise_rmsd.html