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martimunicoy / peleffy

The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.

Home Page:https://martimunicoy.github.io/peleffy

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Correction of bad geometries

carlesperez94 opened this issue · comments

commented

We were wondering if peleffy can correct ligands with bad geometries but correct connectivity. This feature would be very useful for FragPELE simulations. I provide here a PDB example with an hydrogen atom in a bad position.

growing_result.txt

commented

I have run a minimization with PELE, getting OPLS2005 templates from the following input pdb structure:

image

I got this output:

image

So seems that we can correct geometries by applying PELE's minimization.