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

From: David A Case <>
Date: Tue, 30 Oct 2018 11:52:25 -0400

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

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 - 09:00:04 PDT
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