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

From: soukaina louerdi <s.louerdi.uhp.ac.ma>
Date: Sun, 28 Oct 2018 18:37:32 +0000

Dear Prof.Case,
Many thanks for your email.
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). but still
need to specify the partial charges of each atom.
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

 I'm getting two files : inprcd and prmtop, but both of these files were
created with:

> check UNL
Checking 'UNL'....

Warning: The unperturbed charge of the unit (-1.002000) is not zero.
Checking parameters for unit 'UNL'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
> saveoff UNL unl.lib
 Creating unl.lib
Saving UNL.
Building topology.
Building atom parameters.
> saveamberparm UNL h_p3ht.prmtop h_p3ht.inpcrd
Checking Unit.

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

Note: Ignoring the warning from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 3 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

res total affected

UNL 1
.




Le dim. 28 oct. 2018 à 02:13, David Case <david.case.rutgers.edu> a écrit :

> On Sun, Oct 28, 2018, soukaina louerdi wrote:
> >
> > I tried to build and lammps dynamic properties of the thiophene polymer.
> > I want to construct a polymer by using Moltemplate with Gaff force field.
> > And I want to generate the partial charges using antechamber (AM1/BCC)
> but
> > i found the error attached to this email.
>
> There was no error attached to the email. There was a message that your
> "UNL" ligand had a charge of +1. (It does look like there might be an
> error message that was cut off at the bottom on the screen shot. It is
> generally better to copy and paste such messages into the body of the
> email.
>
> Note that readers on this list (a) have no idea how you made the unit, and
> (b) don't know if this charge is correct or not.
>
> You would need to provide much more detailed information to get any
> help. Also bear in mind that most people on the list will not be
> familiar with Moltemplate.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


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h_p3ht.png
(image/png attachment: h_p3ht.png)

Received on Sun Oct 28 2018 - 12:00:03 PDT
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