Test errors

[GoogleCodeExporter]

What steps will reproduce the problem?
1. Installed acpype, ambertools12 and tried: /programs/acpype/test$ 
../acpype.py -i FFF.pdb
2.
3.

What is the expected output? What do you see instead?
~/programs/acpype/test$ ../acpype.py -i FFF.pdb 
================================================================================
===============
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-05-23 13:33:29Z Rev: 388 
(c) 2011 AWSdS |
================================================================================
===============
==> ... charge set to 0
==> ... converting pdb input file to mol2 input file
==> * Babel OK *
==> Executing Antechamber...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

---Judge bond type for Residue 1 with ID of 1 and Name of PHE ---

---Judge bond type for Residue 2 with ID of 2 and Name of PHE ---

---Judge bond type for Residue 3 with ID of 3 and Name of PHE ---
Running: /home/oliver/programs/amber12//bin/bondtype -j full -i 
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac

Running: /home/oliver/programs/amber12//bin/atomtype -i ANTECHAMBER_AC.AC0 -o 
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 244; net charge: 0

Running: /home/oliver/programs/amber12//bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/oliver/programs/amber12//bin/sqm -O -i sqm.in -o 
sqm.out" of bcc() in charge.c properly, exit

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Antechamber failed
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -i: not found
++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Parmchk failed
ERROR: Tleap failed
==> ... trying Sleap
==> Executing Sleap...
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
/bin/sh: -f: not found

++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
ERROR: Sleap failed
==> Removing temporary files...
ACPYPE FAILED: [Errno 2] No such file or directory: 'FFF_AC.prmtop'
Total time of execution: 27s

What version of the product are you using? On what operating system?
Latest version of acpype 6th July 2012 on  Ubuntu 10.04 LTS - the Lucid Lynx 

Please provide any additional information below.
Not sure if there is support for these kinds of problems or if I should be 
posting my problems here or elsewhere?

Original issue reported on code.google.com by Olivercg...@gmail.com on 6 Jul 2012 at 12:54

[GoogleCodeExporter]

Please, read the FAQ.

Original comment by alanwil...@gmail.com on 22 Jul 2013 at 12:40

[GoogleCodeExporter]

Original comment by alanwil...@gmail.com on 22 Jul 2013 at 12:41

• Changed state: Fixed