Re: [AMBER] the unperturbed charge of the unit is not zero

From: Charu Sharma (JRF) <"Charu>
Date: Tue, 30 Oct 2018 21:56:11 +0530

Respected sir,
I am getting hurdle in this why it is not loading the molecule?

On Tue, Oct 30, 2018 at 9:22 PM David A Case <> wrote:

> On Tue, Oct 30, 2018, soukaina louerdi wrote:
> > Please you will find attached files of 3 Molecules
> OK...some progress.
> First, antechamber is apparently ignoring the "-m" flag. (CC-ing to
> Scott for investigation.) So, you are indeed getting a closed shell ion
> calculation.
> Second, you asked for a net charge of +1 ("-nc 1") which corresponds to
> removing a hydride from the parent molecule. The charges one gets
> indeed sum to +1. It's unclear what you did later on to get a charge
> inside tleap of -1, but that may be uninportant: you can always look in
> the mol2 file for the actual charges being used.
> Third, neither +1 or -1 is likely to be correct for a polymerization
> modeling: I'm guessing that two neutral radicals coming together is more
> likely to be what you want. So you may just want to get charges for the
> parent molecule, remove the appropriate hydrogens (which will have small
> net charges) and manually redistribute the excess charge over the
> molecule, so that each unit has zero charge.
> ...hope this helps...dac
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Received on Tue Oct 30 2018 - 09:30:03 PDT
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