Re: nmode segmentation fault

From: Holger Gohlke <>
Date: Thu 08 Aug 2002 11:16:11 -0700

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
              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


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
Received on Thu Aug 08 2002 - 11:16:11 PDT
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