AMBER Archive (2002)

Subject: Re: nmode segmentation fault

From: Haizhen Zhong (zhongh_at_umich.edu)
Date: Fri Aug 09 2002 - 08:46:19 CDT

Dear Dr. Gohlke:

This is Haizhen. Thank you very much for your help. After the modification
as you said, the nmode runs very well. Thank you very much.

Yours,

Haizhen

On Thu, 8 Aug 2002, Holger Gohlke wrote:

> Dear Haizhen,
>
> > However, it gave me the core
> > dump file. Another point I want to point out is that no matter I ran it in the
> > formatted or unformatted form, it gave me the same result. THat means, the
> > minimization step was always ok, but the nmode step was always not ok. The
> > related .in file is attached as follows. By the way, the system is around 88
> > amino acids to 99 amino acids.
>
> You traced a problem of memory allocation which occurs in nmode of
> amber6, but has been removed in nmode of amber7. Please replace in
> amber6/src/nmode/alloc.f the lines:
> >>>
> c ---need at least four scratch arrays
> c of size ns3 for thermo
> nvect4 = max(nvect,4)
> memusd_x = mcvec + ns3*nvect4*mprec
> <<<
> with
> >>>
> memusd_x = mcvec + ns3*ns3*mprec
> <<<
> and recompile nmode.
>
> We will also put this as bugfix.28 for amber6 to the amber home page.
>
> Best regards
>
> Holger
>
> --
> +++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Dept. of Molecular Biology, TPC15
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> La Jolla CA 92037 USA
> phone: +1-858-784-9788
> fax: +1-858-784-8896
> email: gohlke_at_scripps.edu
> +++++++++++++++++++++++++++++++++++++++++++++
>