Hi Lenka,
There are ions in the selected file yes, but because its NaCl, there are
equal amounts Na+ as Cl-, so it will be neutral. I think the answer to your
first question will resolve the second, but i am unsure whether you are
also referring to building the protein in tleap or something with the
actual MD.
Hopefully that helped.
Clorice
On Tue, Mar 31, 2020 at 6:28 PM Lenka <Vellryba.seznam.cz> wrote:
>
> Hi,
>
>
>
>
>
> I am to simulate protein in 0.15M NaCl. It is a membrane protein so I
> build
> the membrane in Charmm and generate files for Amber.
>
>
>
>
>
> Despite the fact I select 0.15M NaCl, I get this message in the min_mdout
> file:
>
>
>
>
>
> Sum of charges from parm topology file = 0.00000000
> Forcing neutrality...
>
>
>
>
>
> Shouldn't there be a charge present in the parm file if the ions add to 150
> mM NaCl? There are ions present in the generated pdb.
>
>
>
>
>
> My second question is, if I select the charge will the Amber PME
> calculation
> neutralize the charge anyway? I was under the impression that this happens
> so how can you run a simulation at 0.15M?
>
>
>
>
>
> Thank you for the explanation
>
>
>
>
>
> L.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 31 2020 - 16:00:02 PDT
