After adding ions i gave the desc command then it gave the following:
*Head atom: null *
*Tail atom: null *
*Contents: *
*R<RG5 1> *
*R<RC 2> *
*R<RC3 3> *
*R<OAU 4> *
*R<RG 5> *
*R<RC3 6> *
*R< Na+ 7> *
*R<**Na+ 8**> *
*R<**Na+ 9**> *
*R<**Na+ 10**> *
*R<**Na+ 11*
*Sir may I know how to interpret the above data.*
On Tue, Aug 25, 2015 at 6:13 PM, Kasprzak, Wojciech (NIH/NCI) [C] <
kasprzaw.mail.nih.gov> wrote:
> Martina,
>
> I have seen this error (exactly the same fractional left-over charge) with
> modified RNA nucleotides at the terminal
> positions. No terminating hydrogen was added by leap at the 3' end, and
> the 5' end contained
> the full phosphate group.
> I did not have the params for terminal versions of the modified nts and
> gave up on modifications at these position
> because they were not essential to our simulations. Then the net charge
> was neutralized. It's and observation and
> a "bypass" option, but perhaps it will elicit more comprehensive
> explanation and a proper fix idea from other users.
>
> Good luck, Voytek
>
> Wojciech (Voytek) Kasprzak [Contractor]
> Analyst Programmer,
> Basic Science Program, Leidos Biomedical Research, Inc.
> Frederick National Laboratory for Cancer Research, Frederick, MD.
> (301) 846 5537
> http://binkley2.ncifcrf.gov/users/kasprzak
> ________________________________________
> From: David A Case [david.case.rutgers.edu]
> Sent: Tuesday, August 25, 2015 8:15 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] how to neutralized my system with Na+ ions
>
> On Tue, Aug 25, 2015, Martina Devi wrote:
> >
> > I have been trying to neutralize my system whic has a non-standard base
> > with Na+ ions.
>
> > ERROR:The unperturbed charge of the unit: -0.691900 is not integral.
>
> This looks like the charge of the non-standard base is not an integer.
> You can use the "check" command in tleap to sum the charges of a given
> unit.
> The desc command will show you what the charges are.
>
> ....dac
>
>
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Received on Tue Aug 25 2015 - 07:00:03 PDT
