Thank you David. We are looking into it.
On Mon, 19 Mar 2018, 13:07 David A Case, <david.case.rutgers.edu> wrote:
> On Mon, Mar 19, 2018, maryam azimzadehirani wrote:
> >
> > I am preparing glycosylated and unglycosylated
> > models of a receptor. while making the unglycosylated solvated model I
> > need 4 NA+ to neutralize the system but when I am trying to
> > solvate glycosylated proteins 3NA+ ions were required for
> > neutralization (3.6 NA+ to be precise, and leap added 3 ions to the
> system,
> > I am not sure why 3 and not 4).
>
> You need to try to figure out why the charge is non-integral: add up the
> charges of the glyocosylated residue by itself. If that is not an
> integer, something is going wrong with that residue. We would need to
> know details about how you prepared your system. (I could not follow the
> discussion that led to one system having a net charge of -3.6, and
> another a net charge of -5.7, for example).
>
> You might consider asking your question at the GLYCAM site, since they
> are most likely to be the people that will know what to do.
>
> ...good luck....dac
>
>
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Received on Mon Mar 19 2018 - 08:00:03 PDT
