[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Melchor S.]

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.