Nmode recompilation

From: Thomas Steinbrecher <thomas.steinbrecher.physchem.uni-freiburg.de>
Date: Tue, 01 Jul 2003 10:41:33 +0200

Dear AMBER users,

I want to perform a normal mode analysis on a protein
ligand complex with ~5000 atoms.

I found several mails in the archive concerning this,
stating that you would need ~2GB of memory for such a
calculation. This amount of RAM was beyond the range of a
PC at that time, but is possible now.

However if I compile nmode with MAXMEMX=350.000.000 in
sizes.h, I get the compiler error:

         real*8 x (MAXMEMX)
Array `x' at (^) is too large to handle
make: *** [nmode.o] Fehler 1

Is it possible to compile nmode in a way that lets it use
some GB of memory?

Can anyone give me a hint if there are any other ways to
perform a normal mode analysis on a protein-ligand complex
and how to do it? (For example something like the treatment
of a reduced complex. I asked about that yesterday.)

Many thanks in advance,

Thomas Steinbrecher
Received on Tue Jul 01 2003 - 09:53:01 PDT
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