Re: [AMBER] how to neutralized my system with Na+ ions

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Tue, 25 Aug 2015 12:43:08 +0000


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
From: David A Case []
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.


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Received on Tue Aug 25 2015 - 06:00:02 PDT
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