[Dock-fans] Error: the output file, output_conformers.1.prmtop, is not complete !

Scott Brozell sbrozell at rci.rutgers.edu
Thu Oct 28 11:17:13 PDT 2010


Hi,

On Thu, Oct 28, 2010 at 10:39:40AM -0600, Andrea L Edwards wrote:
> 
> When I undefine AMBERHOME and see
> 
> chem171-223-dhcp:~ andreaedwards$ echo $AMBERHOME
> 
> chem171-223-dhcp:~ andreaedwards$
> 
> I get the error 
> 
> >>>> Error from amberize_ligand; the name of the ligand is
> >>>>   ZINC04228232
> >>>>   Examine amberize_ligand.output_conformers.1.out
> 
> and the output is :

--------------
Using ligand file prefix: output_conformers.1
Using antechamber options: -nc 0 -c bcc
Executing antechamber to generate the mol2 file with GAFF and charges.


Total number of electrons: 202; net charge: 0 
Running: $DOCK_HOME/bin/mopac.sh
ln: FOR005: Operation not supported  INPUT FILE MISSING OR EMPTY
mv: rename FOR006 to mopac.out: No such file or directory
Cannot open mopac.out , exit
Running: 
/Network/Servers/riboswitch.colorado.edu/bateyhome/andreaedwards/Downloads/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full 
Running: /Network/Servers/riboswitch.colorado.edu/bateyhome/andreaedwards/Downloads/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff Error running antechamber! 
--------------
 
This means that undefining AMBERHOME is a correct step towards fixing
the problem; note that mopac, not divcon, is being called by antechamber.
However, it appears that something is amiss with mopac.
It may be necessary to edit dock6/bin/mopac.sh following the comments
in that file, but first check the existing mopac input files,
then remove the mopac input files, rerun prepare amber,
and if it does not work then send the directory listing and the mopac
input files:
rm mopac.in FOR0?? mopac.out

scott



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