Automation for Energy Minimizing protien structure
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2.4 years ago

I have nearly 100 pdb structures to be energy minimized. I need a tool or script to run multiple energy minimization at a stretch. My actual work is to predict the changes in function of a protein with few mutations. So I m in search of automating this process. This is ligand-protein structure.

protein gromacs structure energy minimization • 798 views
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2.4 years ago
fracarb8 ▴ 300

Have a look at gromacs (http://www.gromacs.org/). You can either use bash to wrap the gromacs calls (as I did) and batch process the pdbs or you can have a look at one of the wrappers on github. There is a bit of set up to do, but their documentation is quite good.

You may want to consider running some docking or MD simulations if you want to full study the ligand-protein bind over time.

During my Phd I study the effect of single point mutation of a protein structure, and gromacs was my tool of choice.

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I have been using gromacs for energy minimization following some tutorial (Tutorial link:http://www.mdtutorials.com/gmx/complex/index.html ) But i have to manipulate the topology files manually for that reason only I m searching for some GUI based or any scripts.Please go through the step in the link above and give me a suggestion to automate that tutorial.

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It depends a bit where your mutations are. The topology of your 100 proteins are likely to be exactly the same, but for few residues. You can generate the topology for the wild-type and then replace the coordinates of the mutate residues, to obtain all the mutants you want.

The quickest way could be to use the "mutagenesis" function in pymol to mutate your residues programmatically (see https://pymol.org/dokuwiki/doku.php?id=api:cmd:wizard). A few lines of python should do the trick.

You can then replace the new coordinates using sed

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Thanks for your reply. i have all the mutated pdb files now. I have to perform energy minimization for all the mutated structures. I cant run gromacs for all mutated structures one by one so I have to find a way for automating that.

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bash is your friend here :D I would suggest to have a look at github as there are several gromacs wrappers (e.g. GromacsWrapper).

If you need inspiration to write your own piece of code, you can have a look at the project I used.

Note that it is massively outdated: doitGROMACS_equilib

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does the code will minimize the structure of ur git hub code