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

From: David A Case <>
Date: Mon, 29 Oct 2018 08:07:46 -0400

On Sun, Oct 28, 2018, soukaina louerdi wrote:

> I use Avogadro to make a Molecular model (3-hexylthiophene* ( *C10H15S) )
> and I get Pdb file (I have attached an image of the pdb file).

Attaching the pdb file itself would be much more helpful, since we could
try to reproduce the problem. But it looks like you are missing a
hydrogen atom on a carbon atom in the ring.

> Based on the Antechamber tutorial (sustiva) :
> $AMBERHOME/bin/antechamber -i h_p3ht.pdb -fi pdb -o h_p3ht.mol2 -fo mol2
> -nc 1 -m 2 -c bcc -s 2 -j 5

The fact that you requested a multiplicity of 2 suggests that you
intended to leave out the hydrogen, but gaff is designed for closed
shell molecules. What is this ligand supposed to interact with? Does
it polymerize with a second identical molecule? It's hard for me to
figure out how you can have a odd number of electrons and yet a net
charge of +1....but I could well be missing something from the
screenshot you sent.

> Warning: The unperturbed charge of the unit (-1.002000) is not zero.

This is indeed odd, since you requested a net charge of +1, but got a
net charge of -1.


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Received on Mon Oct 29 2018 - 05:30:03 PDT
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