Hello All,
I'm attempting to create a lipid bilayer, but I am running into problems with the solvation and neutralisation. The bilayer normal is parallel to y (an artefact left over from my having built it in Chimera) in the LEaP script copied below. If I add the correct number of Na+ to neutralise BEFORE solvating, the Na+ ions that wind up around the perimeter of the acyl chains get treated like solute, and I get a layer of water around this perimeter, too, upon solvating.
If, instead, I solvate FIRST, then addIons (or addIons2), as near as I can tell, the oxygens get deleted where steric clashes occur, but NOT their respective hydrogens. Inspection of the resulting mol2 file looks like spirograph gone mad in the water region, with lots of zigzags connecting Na+ atoms to far flung coordinates somewhere, too. This is presumably due to the connectivity problems after re-indexing the serial numbers for Na+ vs the original oxygen serial numbers.
Is this a bug, or have I done something daft? "Daft" is entirely possible — I had a week's introduction to AMBER ~two years ago, on a simple peptide, and I'm only just getting back into it. I've combed the manuals and archives, but couldn't find anything that made the difference.
Many thanks for your help,
John
logFile tleapPCL80.log
source leaprc.ff99SB
source leaprc.lipid11
loadOff PCL.lib
PCL80 = loadPdb "PCL80init.pdb"
solvatebox PCL80 TIP3PBOX {0.0 20.0 0.0} 1.0
addIons PCL80 Na+ 160
saveAmberParm PCL80 PCL80.prmtop PCL80.inpcrd
saveMol2 PCL80 PCL80.mol2 1
quit
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John Gehman Office +61 3 8344 2417
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have defeated smallpox. Never."
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Received on Wed Mar 20 2013 - 07:30:06 PDT
