Acpype errno2

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Entered a small pdb file of a ligand

2. Typed acpype.py -i ligand.pdb

What is the expected output? What do you see instead?

The topology of the ligand.

What version of the product are you using? On what operating system?

The latest, i am using it on a linux based cluster interface.

Please provide any additional information below.

| ACPYPE: AnteChamber PYthon Parser interfacE v. 0 0 Rev: 0 (c) 2014 AWSdS |
============================================================================
==> ... charge set to 0
WARNING: Old version of antechamber. Strongly consider upgrading to AmberTools
WARNING: Setting mopac for antechamber
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Info: Bond types are assigned for valence state 20 with penalty of 2
sh: /share/apps/ambertools/bin/mopac.sh: No such file or directory
Running: /share/apps/ambertools/bin/bondtype -j full -i 
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /share/apps/ambertools/bin/atomtype -i ANTECHAMBER_AC.AC0 -o 
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 176; net charge: 0

Running: /share/apps/ambertools/bin/mopac.sh
Error: cannot run "/share/apps/ambertools/bin/mopac.sh" of bcc() in charge.c 
properly, exit

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Cannot open file 5-licam_bcc_gaff.mol2 to read in rmol2(), exit
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -c: line 0: syntax error near unexpected token `('
/bin/sh: -c: line 0: `which: no sleap in 
(/share/apps/intel/composer_xe_2011_sp1.10.319/bin/intel64:/share/apps/gromacs/b
in:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/loca
l/sbin:/usr/sbin:/sbin:/opt/eclipse:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/java
/latest/bin:/opt/maven/bin:/opt/pdsh/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/gri
dengine/bin/linux-x64:/share/apps/intel/composer_xe_2011_sp1.10.319/mpirt/bin/in
tel64:/home/nmichelarakis/bin:/share/apps/bin:/share/apps/TURBOMOLE_6.40/scripts
:/share/apps/TURBOMOLE_6.40/bin/em64t-unknown-linux-gnu:/share/apps/openbabel/bi
n/:/share/apps/nbo4.9/:/share/apps/cmake/bin:/share/apps/cuda/bin:/share/apps/jm
ol/:/share/apps/tinker/bin:/share/apps/molden:/share/apps/fftw/lib:/share/apps/c
pmd:/share/apps/tcl/bin:/share/apps/chemshell/bin:/share/apps/chemshell/scripts:
/share/apps/orca:/share/apps/ambertools/bin:/share/apps/acpype) -f sleap.in'

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: '5-licam_AC.prmtop'
Total time of execution: less than a second

Original issue reported on code.google.com by nm...@york.ac.uk on 4 Aug 2014 at 3:10

[GoogleCodeExporter]

I met the same problem when using Acpype with old version of Antechamber 
(AmberTools12). And I have come up a workaround that works for me.

Based on the discussion in 
https://code.google.com/p/acpype/issues/detail?id=16, 2nd WARNING: "Setting 
mopac for antechamber" means Acpype are looking for mopac instead of sqm for 
the atomic partial charge calculation. However, mopac is non-existing in 
AmberTool, therefore causing the problem.

My workaround is adding partial charge calculation option (-c) when executing 
acpype (i.e. ./acpype.py -i input.mol2 -c user), which will overlook the step 
of looking for default partial charge calculation program, so process the rest. 
You can alway use other more sophisticated methods to obtain the atomic partial 
charge such as RESP fitting and such.

Original comment by supermep...@gmail.com on 10 Jul 2015 at 5:23