Re: [AMBER] Error: Unable to run flex; this is required for NAB and antechamber Please check your PATH, or install the program

From: David A Case <>
Date: Fri, 13 Mar 2015 07:06:53 -0400

On Fri, Mar 13, 2015, vijay kumar narsapuram wrote:
> 1) After going through amber manual I came across "kappa" keyword
> k=(0.10806I)1/2,where "I" is ionic strength which is in [M].
> is this keyword anyway helpful in calculating saltcon for my system.

Various Amber programs are not completely consistent here. Basically, saltcon
(ionic strength) and kappa are equilvalent variables: if you know one you can
compute the other. Some programs ask for saltcon on input, and some for

> 2) In the paper they discussed about salt contribution in GB
> theory,but I didn't get any of the formula related to saltconc
> calculation.

Please consult Ref. 122 in the Amber14 Reference Manual.


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Received on Fri Mar 13 2015 - 04:30:02 PDT
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