AMBER Archive (2004)

Subject: Re: AMBER: tutorial of Biotin/Streptavidin

From: David A. Case (
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, 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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to