I just noticed that while adding “CL” neutralised the charge just fine, however there are seemingly two “default” options, CL and Cl-.
Looking at these options it seems that CL would be “atom” and Cl- “anion”. However, the only example i found for addIons with chloride in the manual used “CL”, making it less likely that this would be the "bonded” state, assuming the “atom” state would be unreasonable. Reusing this option also neutralised the charge.
Am I safe to assume that using “Cl-" would be more appropriate choice with “addIons” (is there any difference)? In that case the remaining issues with reading back a PDB file stems from “packmol” residue numbering and all “problems” have been solved.
Looking at the 3.6 Ions section, is there any reason to source modifications for use with OPC (or TIP3P/ SPC-E for that matter).
For leaper.water.opc:
Monovalent ion parameters for Ewald and TIP4P/EW water from Joung & Cheatham JPCB (2008)
Loading parameters: /Users/guolaa/SOFTWARE/amber20/dat/leap/parm/frcmod.ions234lm_126_tip4pew
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP4P/EW water model (12-6 normal usage set)
Though according to the manual:
Two sets of 12-6 LJ parameters for OPC water model (the 12-6 IOD set and the 12-6 HFE set) for 3 monovalent ions (Na+, K+, Cl-) have been developed…
These are not loaded, instead what is described in the manual:
Based on our limited experience, it appears that the Joung/Cheatham ion parameters for TIP4P-EW may be acceptable
Can one safely assume that the parameters loaded with leaper.water.opc/spce/tip3p are reasonable with regard to Cl-?
Best regards
// Gustaf
> On 21 Oct 2020, at 09:04, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> 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 - 05:30:03 PDT
