Dear Rebeca,
as the message states this is only for informational purposes to the
user. If antechamber had thought that there is a problem with your
input you would have gotten a "Warning" message.
Atom and bond type assignment is not a trivial task and conflicts
may arise when doing so. You may want to read the original paper on
antechamber to understand what this penalty really means but basically
antechamber thinks that everything is fine. It may not hurt though to
go through the generated atom types and look for yourself if assignment
is sensible.
Cheers,
Hannes.
On Fri, 13 Mar 2015 09:24:20 +0000
Rebeca García Fandiño <regafan.hotmail.com> wrote:
> Dear Amber users,
> I am trying to parametrize the cation from propidium iodide
> (http://en.wikipedia.org/wiki/Propidium_iodide) using Antechamber. It
> has a positive charge of +2. I get this message:
>
> $AMBERHOME/exe/antechamber -i minimizado.mol2 -fi mol2 -o
> minimizado.ac -fo ac -nc 2
>
> Info: Bond types are assigned for valence state 1 with penalty of 1
>
> I have read some answers to problem related, such as atoms
> missing....but it is not my case, I have checked the structure and
> all seems to be OK.
>
> I am using Ambertools in Amber11 and I have also tried in Amber12 and
> the error is the same.
>
> Any help would be much appreciated!!
>
> Best wishes,
>
> Rebeca.
>
> Dr. Rebeca Garcia
> Santiago de Compostela University
> Spain
>
>
>
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Received on Fri Mar 13 2015 - 03:30:02 PDT
