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

From: soukaina louerdi <s.louerdi.uhp.ac.ma>
Date: Tue, 30 Oct 2018 12:18:04 +0000

Dear Prof Case,

Thanks for your email
Please you will find attached files of 3 Molecules


Le mar. 30 oct. 2018 à 12:10, David A Case <david.case.rutgers.edu> a
écrit :

> On Tue, Oct 30, 2018, soukaina louerdi wrote:
> >
> > My goal is to construct Polymer P3ht "C10H14S" (Degre of polymerization
> 50)
> > using Moltemplate ( is a general molecule builder and Force Field
> database
> > system for lammps), specifying coordinates, partial charges .. of each
> atom
> > of the monomer.
> > My idea is to create 3 Monomers :
> > - 2 Monomers of end chain ( attached to this mail )
> > - 1 Monomer (attached to this mail)
> > I had coordinates but still need to specify the partial charges of each
> > atom.
>
> As I mentioned before, it does very little good to send just an image of
> the molecule: one would need the actual pdb file to try to reproduce the
> problem you reported before. In particular, I can't figure out from the
> image file how h_p3ht could have a charge of +1 *and* an odd number of
> electrons.
>
> The general problem is this: the am1-bcc charge model is designed for
> closed-shell molecules. It's probably not all that bad for radicals,
> but it's never been tested. You might want to use resp charges instead,
> since they are a little more general. But it might not make much
> difference.
>
> ....dac
>
>
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Received on Tue Oct 30 2018 - 05:30:03 PDT
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