Workaround: why not substitute a 3-letter name, packmol it, then
resubstitute?
Bill
On 10/20/20 5:56 AM, Gustaf Olsson wrote:
> 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 - 07:00:03 PDT
