[Chimera-users] help with antechamber

[Eric Pettersen]

Hi Philip,
	As far as we know, this problem only occurs in 32-bit daily builds from before January 25th of this year.  Does this match up with the version you’re using?  If not, first:  try the current daily build.  If that doesn’t work, let me know (and whether you used the 32- or 64-bit build).

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Mar 12, 2016, at 7:49 AM, Philip Hanley <philiphanley at outlook.com> wrote:
> 
> To whom it concerns,
> I’ve been using antechamber as part of a university project. I’m away from the university for the next few weeks and have downloaded chimera on my mac. I was using chimera on linux in the university. 
> Im having the same issue, irregardless of what molecule i have, which is dock prep / add charge. I’m following the same procedure as i did in the university with molecules i know add charge did work for, but am receiving the following error;
> 
> Charge model: AMBER ff99SB
> Assigning partial charges to residue TAG (net charge +0) with am1-bcc method
> Running ANTECHAMBER command: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.in.mol2 -fi mol2 -o /var/folders/4n/vv33g5cj65175vlsgg86_0h00000gn/T/tmpm0Jyho/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2
> (TAG) 
> 
> (TAG) dyld: Library not loaded: /usr/local/lib/libquadmath.0.dylib
> 
> (TAG)   Referenced from: /Applications/Chimera.app/Contents/Resources/lib/libgfortran.3.dylib
> 
> (TAG)   Reason: image not found
> 
> (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> 
> (TAG) 
> 
> (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> 
> (TAG) Total number of electrons: 98; net charge: 0
> 
> (TAG) 
> 
> (TAG) Running: /Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out
> 
> (TAG) Error: cannot run "/Applications/Chimera.app/Contents/Resources/bin/amber14/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit
> 
> Failure running ANTECHAMBER for residue TAG
> Check reply log for details
> 
> Is there anything possible wrong with the general settings in the program that have to be changed? i have literally installed chimera, and changed no settings thus far. I have looked up forums relating to similar issues but have no found a solution.
> 
> Any help would be highly appreciated, 
> thanks in advance, 
> phil
> 
> 
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