Re: AMBER: understanding SANDER source code

From: Andreas Svrcek-Seiler <>
Date: Mon, 22 Mar 2004 13:15:42 +0100 (CET)

> I am trying to understand sander source code line by line, and find it's
> rather frustrating. Can anyone share his/her experience? Or where can I find
> the basic frame, like a flow chart, for sander. Thanks!
....for a start, you could download NAB
(http:// The force field based routines
contained in NAB comprise only a small fraction of the stuff in sander,
but are easy (?) to read and to follow (look into "sff.c").
Besides, they are completely "AMBER compatible".
Tinker (from: is also a good choice for
learning from the sources (as was already pointed out).
This is one of the rare instances where one "bloated" source file (sff.c)
might be preferred over many nicely separate source files (as in tinker or
AMBER), at least if you are trying to follow the program.
You might compile NAB (with "-g3" in the CFLAGS, OCFLAGS and NABFLAGS) and
even follow some MD-examples with your debugger.
If you understand sff.c, it's much easier to understand sander and all
it's modules afterwards (my experience).

good luck,

           ( O O )
              o        Wolfgang Andreas Svrcek-Seiler  
              o        (godzilla) 
      .oooO            Tel.:01-4277-52733 
      (   )   Oooo.    
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Received on Mon Mar 22 2004 - 12:53:00 PST
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