vdw clashes

[SalahBioPhysics]

@gregoryross Here is a list of vdw clashes that are above 10 kCal/mol of 4G5J (Afatinib)

4G5J_vdw_clashes.xlsx

For the ligand if the protons do not have charges they can be removed. I need to check that.

[SalahBioPhysics]

@gregoryross do you have the vdw radii and potentials you used for the structure relaxation?

[mrgunner]

can be make the time to think about how to deal with vdw play with the phi map thanks m

On Jan 31, 2017, at 9:32 PM, Salah Salah notifications@github.com wrote:

@gregoryross https://github.com/gregoryross do you have the vdw radii and potentials you used for the structure relaxation?

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[gregoryross]

Hi @SalahBioPhysics,

Thanks for the file. I'm currently looking at the 4G5J-minimized.pdb structure in PDBfinder/pdbs/Afatinib-EGFR/explicit_water_minimized, but I can't match the residue numbers to the PDB. The residues in that PDB go from 1 to 322, but the file 4G5J_vdw_clashes.xlsx lists residue numbers in from 700+. Do you know how the numbering matches up?

As you listed the atoms names and residue names in the excel file, I found the closest pair of PHE HZ and LYS O atoms (the first clash you list) have a distance of 2.62 Angstroms, not 1.84 Angstroms as listed. As the numbering is different, I may have missed which one you meant, but it's possible you may not be using the most up-to-date structures. Could you please check that the structures your using are from the PDBFinder repo under pdbs/*/explicit_water_minimized/*?

[gregoryross]

(Sorry, I didn't mean to close this issue!)

[jchodera]

It might be important to make sure the pdbfixer and/or maestro-based preparation pipelines you guys have preserve the residue numberings. Or was that lost on the MCCE2 side?

[gregoryross]

That's a good point @jchodera. It seems that the latest structures (prepared with Maestro) have re-numbered the residues. That's something we can easily fix.

After a quick look, it seems that you may be looking at one of the older structures that did have vdW clashes. As I stated here, the cleanest structures we've produced can be found in the PDBFinder repo in the pdbs/*/explicit_water_minimization/ directories. Is the spreadsheet you generated for the structure in pdbs/Afatinib-EGFR/fixed/4G5J-fixed.pdb?

[SalahBioPhysics]

I completely missed this, I used the /fixed/ folder, I will fix it and start using pdbs/*/explicit_water_minimization/ folder. Thanks @gregoryross

[SalahBioPhysics]

@gregoryross I ran few proteins from pdbs/*/explicit_water_minimization/ folder and didn't have any vdw clashes. Thanks again @gregoryross 👍

[gregoryross]

You're very welcome @SalahBioPhysics!