Re: nucleic acids - total charge

From: Raghav (raghavbioinfo_at_gmail.com)
Date: Tue May 01 2012 - 11:18:22 CDT

It is the usual psfgen with vmd using top_all27_protein_lipid_na.top.

On May 1, 2012, at 17:48, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> 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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