AMBER Archive (2004)

Subject: Re: AMBER: tutorial of Biotin/Streptavidin

From: David A. Case (case_at_scripps.edu)
Date: Sat Apr 24 2004 - 15:08:00 CDT

On Sat, Apr 24, 2004, Helios Chen wrote:

> Dear all, I do sander accroding to the tutorial of Biotin/Streptavidin to
> mininmize the complex using min.in, I got the following message:

...

> getting new box info from bottom of inpcrd
> | peek_ewald_inpcrd: Box info not found in inpcrd
> compute_nfft: failed to get good fft array size
> x = 4.4184937307205338E+25
>

This tutorial was made for a quite old version of Amber; (who wants to
volunteer to update it?) Since this is a non-periodic simulation, you
need to set "ntb=0" in your input. That used to be the default, but is
not the default any longer. There may be some other things that you need
to tweak as well.

...good luck...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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