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

From: David A Case <>
Date: Tue, 30 Oct 2018 08:08:03 -0400

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

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


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Received on Tue Oct 30 2018 - 05:30:03 PDT
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