Dear AMBER,
I just wanted to make sure my message went through to the list yesterday.
Thanks,
Holly
On Mon, Dec 2, 2013 at 5:46 PM, Hallel Freedman <hfreedma.ualberta.ca>wrote:
> Dear AMBER,
>
> I am setting up AMBER simulations of a proteins containing zinc fingers,
> and I am trying to use the Zinc parameters from Yuan-Ping Pang, together
> with the library and parameters downloaded from the website given on the
> AMBER homepage:
> When I try to save AMBER parm files I am getting messages like:
>
> 1-4: angle 43748 43749 duplicates bond ('triangular' bond) or angle
> ('square' bond)
>
> Is this anything to worry about?
>
> One other thing bothered me a little bit - when I try to solvate the
> system I get messages like:
> (using default radius 1.500000 for D4)
> (using default radius 1.500000 for D3)
> (using default radius 1.500000 for D2)
> (using default radius 1.500000 for D1)
> I suppose this is not important, but I wanted to confirm this with you.
>
> Thanks in advance,
> Holly
>
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Received on Tue Dec 03 2013 - 10:30:04 PST
