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leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen
http://traken.chem.yale.edu/ligpargen/
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distorted phosphate group #9

Open matteoaldeghi opened 6 years ago

matteoaldeghi commented 6 years ago

Issue Information

Software name & Version: Gromacs 2016 Method: plain MD sampling of ligand (mol attached) coordinated to Mg in a solvent box.

Expected Behavior

Actual Behavior

I ran a quick simulation of the ligand attached (TPP.mol), which contains a diphosphate tail and is coordinated to Mg (the ion parameters used were from the OPLS-AA/M force field for Gromacs). I noticed that very quickly the phosphate group gets distorted ("example.pdb" attached; for a comparison I also attached the starting structure "starting.pdb").

I wonder whether it is a force field or a file conversion issue? I noticed for instance that in the Gromacs topology file (ligand.itp) there are a number of torsions with all force constants set to zero.

files.zip

leelasd commented 6 years ago

@matteoaldeghi This might be an issue with Ligand itself. Let me look into it. I will get back to you soon