Re: AMBER: tutorial of Biotin/Streptavidin

From: David A. Case <>
Date: Sat, 24 Apr 2004 13:08:00 -0700

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, 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:
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            |
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Received on Sat Apr 24 2004 - 21:53:00 PDT
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