Hi again, I can give more details about acpype error. This is the error that I obtained,
=============================================================================================== | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | =============================================================================================== ==> ... charge set to 0 ==> ... converting pdb input file to mol2 input file ==> * Babel OK * ==> Executing Antechamber... ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Warning: the assigned bond types may be wrong, please : (1) double check the structure (the connectivity) and/or (2) adjust atom valence penalty parameters in APS.DAT, and/or (3) increase PSCUTOFF in define.h and recompile bondtype.c Be cautious, use a large value of PSCUTOFF (>100) will significantly increase the computation time Running: /home/melchor/Software/amber12/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac Running: /home/melchor/Software/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Total number of electrons: 61; net charge: 0 INFO: Number of electrons is odd: 61 Please check the total charge (-nc flag) and spin multiplicity (-m flag) Running: /home/melchor/Software/amber12/bin/sqm -O -i sqm.in -o sqm.out Error: cannot run "/home/melchor/Software/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: 1: -i: not found ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Parmchk failed ERROR: Tleap failed ==> ... trying Sleap ==> Executing Sleap... ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ /bin/sh: 1: -f: not found ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Sleap failed ==> Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'test_AC.prmtop' So I thought that maybe the problem was my structure but even if I try this tutorial : http://code.google.com/p/acpype/wiki/TutorialAcpype4Gromacs, I obtain a similar error: =============================================================================================== | ACPYPE: AnteChamber PYthon Parser interfacE v. 2012-09-13 14:55:47Z Rev: 389 (c) 2012 AWSdS | =============================================================================================== ==> ... charge set to 0 ==> ... converting pdb input file to mol2 input file ==> * Babel OK * ==> Executing Antechamber... ==> * Antechamber OK * ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ /bin/sh: 1: -i: not found ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Parmchk failed ERROR: Tleap failed ==> ... trying Sleap ==> Executing Sleap... ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ++++++++++start_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ /bin/sh: 1: -f: not found ++++++++++end_quote+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ERROR: Sleap failed ==> Removing temporary files... ACPYPE FAILED: [Errno 2] No such file or directory: 'Ligand_AC.prmtop' Total time of execution: 13m 3s Someone could help me? Is something about the configuration ? Thanks in advance, -- View this message in context: http://gromacs.5086.x6.nabble.com/Problem-with-Amber99SB-ILDN-ff-tp5009641p5009926.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists