Hello mailing list
I am trying to construct a system which needs to include a chloride anion to neutralise positive charge.
Doing this in leap with the addIons command works and I am left with a topology and input coordinate file which according to “parmed" has the correct charge (0) and everything looks OK.
Now, I would like to be able to place the ion in the system using packmol. This is where I run into problems.
Writing out a PDB file from leap or parmed produces this
HETATM 1 CL CL 2 5.829 9.056 -1.558 0.00 0.00 CL
This is not usable when trying to build the system with packmol as there is no way to use a two letter abbreviation in a PDB file and read it correctly back into leap, causing all kinds bad.
Is there a reason why I should NOT place the ion in the system using packmol? If not, how can I create a PDB file for a singe Cl- ion, place it in the system using packmol and have a readable file in leap?
Should I do something similar to “WAT = SPC”, as in naming the chloride ion CLX (for example) and setting CLX=CL?
Any help appreciated
Best regards
// Gustaf
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Received on Tue Oct 20 2020 - 06:00:03 PDT
