Hello Bill, nice to hear from you.
No-go, this might be a problem with the PDB format. Packmol can handle CL just fine, that is not a problem though even if I pack the system with CLX (for example) and then exchange CLX -> CL, the read-frame seems to be is messed up in leap and I end up with errors.
I just used the addIons command instead though this has two effects which could negatively affect the outcome. First, it replaces a solvent molecule and second, you may want to be able to “place” the ion at particular coordinates in the system. Neither of these are of any importance to me right now though I suspect that there is a workaround to be able to use packmol (or something else) to place an ion at a particular coordinate and in this way not removing anything.
All the best
// Gustaf
> On 20 Oct 2020, at 15:48, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> 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 Wed Oct 21 2020 - 00:30:02 PDT
