Re: [AMBER] Boost not linking when compiling on Mac

From: Gustaf Olsson <>
Date: Wed, 2 May 2018 12:53:36 +0000

Right. So, since I can’t go on working I just had to see if I could recreate the issue and I did.

I am assuming the answer to this one will be the same as for antechamber. Since I did not document the issue properly last time and just “guessed” what the output was, I apparently missed the "Fatal Error!” declaration, being this now I would assume that this is just as much of an non issue as the antechamber error.

This time is was an incorrect molecular abbreviation that seemed to cause the error:

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
Warning: This molecule has no hydrogens nor halogens.
         It is quite possible that there are unfilled valences.
-- Check Geometry --
      for those bonded
      for those not bonded
   Status: pass
-- Check Weird Bonds --
   Status: pass
-- Check Number of Units --
   Status: pass
acdoctor mode has completed checking the input file.

Info: Total number of electrons: 0; net charge: 0

Running: /Users/guolaa/SOFTWARE/amber18/bin/sqm -O -i -o sqm.out
/Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Cannot properly run "/Users/guolaa/SOFTWARE/amber18/bin/sqm -O -i -o sqm.out".

It’s just the fatal error that is called from "to_be_dispatched/antechamber” right?

Anyway, thank you for you help and input, let me know if there is anything I can do to help further.
// Gustaf

On 2 May 2018, at 13:48, David A Case <<>> wrote:

On Wed, May 02, 2018, Gustaf Olsson wrote:

/Users/guolaa/SOFTWARE/amber18/bin/to_be_dispatched/antechamber: Fatal Error!
Number of arguments is odd - arguments must come in pairs.

Antechamber does point to the correct location however the error for
antechamber refers to “to_be_dispatched”.

This is expected behavior: the actual antechamber binary executable
lives in $AMBERHOME/bin/to_be_dispatched. I think the reference to
"to_be_dispatched" is unlikely to cause much confusion, but it may be
that we can tweak the "Fatal error" message.

Note that the binary file for sqm does *not* reside in to_be_dispatched,
and the error you reported for it was different than the one above. I
guess we still don't know how the sqm problem arose.


AMBER mailing list<>

AMBER mailing list
Received on Wed May 02 2018 - 06:00:11 PDT
Custom Search