AMBER Archive (2006)

Subject: Re: AMBER: Unable to find mopac charges in divcon.out

From: Mark Williamson (Mark.Williamson_at_imperial.ac.uk)
Date: Thu Nov 23 2006 - 16:06:35 CST

>
> I have spent some time searching in the maillist, haven't got any clues
> to fix it. Thank you in advance for any suggestions.
>
> Best regards,
>
> Rachel
>

Hi,

It seems that divcon is crashing as it is being used by antechamber.
Running divcon outside of the Run.ash script may give more information
about the nature of the crash:

1) cd $AMBERHOME/test/antechamber/ash

2) The Run.ash script cleans up after itself, but you need the divcon.in
file that is generated earlier on in the script. Therefore

  a) Edit Run.ash to comment out the following lines like so:

  #/bin/rm -f ANTE* ATOMTYPE.INF BCCTYPE.INF FOR* NEWPDB.PDB PREP.INF \
  # leap.log prmcrd divcon.dmx divcon.rst divcon.in

  b) Run the ./Run.ash so that the above files are created, but not deleted.

3) Now run divcon explicitly using divcon.in as its runtime instructions:

  $AMBERHOME/exe/divcon divcon.in

If this does not provide any more details to solve the problem, you may
get more information if you run divcon inside a debugger (a debugger is
a tool for dissecting a program and is used to track problems). To do
this, you will first need to tell the compiler to add debugging symbols
to the divcon binary when it builds it. One needs to recompile (in the
way that you have done before) with a config.h that has the extra option
set:

cd $AMBERHOME/src/
edit config.h
set the parameter:
  AMBERBUILDFLAGS=" -g"
save it
make clean
make

Now run the debugger on the binary:

cd $AMBERHOME/test/antechamber/ash
gdb $AMBERHOME/exe/divcon
<some text about gdb>
(gdb) run divcon.in
***program crashes***
(gdb) bt

The output from this will give clues on why the program crashes.

I suspect that the machine you're using does not have gdb, hence you
will need to use whatever debugger is present on it. I think the IBM
debugger is called "dbx" and the analogous "bt" command is "where". I
think the "run" command is the same. I have very very little experience
with such IBM machines, hence I'm quite out of my depth. Maybe someone
else on the list could add in here.

The use of a debugger is generally considered advanced for a standard
user and hence may be painful :) You could alternatively run with the
status quo; as long as sander passes all of its tests, and you're not
going to use divcon on that machine you can probably proceed. This is
not optimal, but neither is wasting enormous amounts of time on a
problem that may not need to be solved.

regards,

Mark

http://dumb.ch.ic.ac.uk/~mjw99/
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