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m3g / packmol

Packmol - Initial configurations for molecular dynamics simulations
http://m3g.github.io/packmol
MIT License
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Creating system with receptor + ligand and water as solvent mix... Duplicate atom serial & max # bonds exceeded errors #60

Closed ONISniperOne closed 3 months ago

ONISniperOne commented 3 months ago

Hello,

I'm trying to surround a receptor with solvent mix of ligand + water in 10:1 ratio (no ligand in binding site). When I open the resulting pdb with saved CONECT records in VMD and ChimeraX, I get max # of bonds exceeded and duplicate atom serial, respectively. The original ligand and receptor files have their own CONECT records.

ChimeraX image

VMD image

Included in the zip file is my receptor, ligand, water, and input file. Thank you! PackMol 10.189.zip

ONISniperOne commented 3 months ago

Update: I reduced the amount of solvent by 2. Now I'm running with 100 waters and 1000 ligands. No more serial id and max # of bonds errors. I guess it was because I had too much solvent in a small space....

lmiq commented 3 months ago

Did Packmol ended with the "Success!" message in the case where you see the problem? If not, probably the system is too dense indeed.

If you want to study in details the interactions of these solvents with the protein, checkout our package: https://m3g.github.io/ComplexMixtures.jl

ONISniperOne commented 3 months ago

I've been slowly reducing the # of solvent molecules while still keeping a 10:1 ratio and the volume box the same. It's a little aggravating. I'm planning to run MD with Amber after creating the initial system - skipping the solvation with tleap.

Thank you for your help! Your tool is very useful. Will cite and post here if there's a publication