Re: nucleic acids - total charge

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 01 2012 - 10:48:19 CDT

Post the psfgen script you're using to build your system so that someone can hopefully identify what you're doing wrong.

On Apr 30, 2012, at 4:55 AM, raghav singh wrote:

> Hi All,
>
> I have a question about total charge of nucleic acid system... no matter what I have tried it does not sum up to an integer value... for a double stranded helix of 24 bp ...i is like 45.9999 ......!! something like this (with terminal patch).
> during ionization it tells me that I have to add 46 ions to neutralize the system... but it come up with some positive value?
>
> while if I understand it right it should be -48 with terminal patch or -47 with terminal patch. (gromacs, amber ).
>
> and after solvation and ionization it comes up with some positive value of 1.23446 ... !!
>
> if someone have any idea abt it.. please tell me how can solve this one.
>
> Thank You
>
> Raghav
>
>

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