I routinely use antechamber for charged molecules and it is not uncommon to receive this warning and needing make minor modifications to the prep file
You’ve already received a lot of valuable feedback though I just wanted to raise a little warning. Unless there is a “typo” in the original post, then you likely have another issue.
> The unperturbed charge of the unit (1.001001)<tel:+441001001> is not zero
This indicates a +1 charge in the system loaded into leap. However:
> my molecule having a -1 charge (-nc 1)
You specify that your molecule should have a “-1” charge yet you specify “-nc 1” which is equal to "-nc +1”. If the “-“ is not a “typo” you need to specify "-nc -1” if your molecule is supposed to be an anion.
You can check the charge in any of a number of ways though if you have awk available, this little one-liner comes in handy for a quick check after running antechamber:
awk '{ sum += $11 } END { print sum } [filename].prep
Best regards
// Gustaf
> On 10 Dec 2020, at 16:01, Sam Walsworth (Researcher) <Sam.Walsworth.hud.ac.uk> wrote:
>
> Hi all
>
> I am aware that you can use antechamber to parameterise charged molecules (using the -nc flag) but I was considering if this is a reliable/tested method? I'm currently going through tLEaP and received an error saying 'The unperturbed charge of the unit (1.001001)<tel:+441001001> is not zero' which I'm assuming corresponds to my molecule having a -1 charge (-nc 1).
>
> My question is how good is antechamber at handling charged molecules? Are these error messages largely trivial or should I be cautious using this method (maybe would manually assigning charges from ab initio calculations be better?)
>
> Sam
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Received on Fri Dec 11 2020 - 00:30:03 PST
