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

Scott Brozell sbrozell at rci.rutgers.edu
Fri Oct 29 00:49:16 PDT 2010


Hi,

What are your system details: os, etc ?

scott

On Thu, Oct 28, 2010 at 02:02:56PM -0600, Andrea L Edwards wrote:
> The contents of mopac.sh are:
> 
> #!/bin/sh
> 
> # Edit the following to match your local environment;  the syntax
> # for calling this shell script should be:  mopac.sh input output.
> # Depending on which version of mopac you have, you may need to remove
> # the "<" and ">" symbols below, or make other changes.  For example,
> # some versions of mopac expect the input file to be "FOR005" and the
> # output to be "FOR006"; some versions require the input file to end in 
> # ".DAT", etc., etc.
> 
> ln mopac.in FOR005
> $DOCK_HOME/bin/mopac
> mv FOR006 mopac.out
> rm -f FOR0??
> 
> I'm not sure what to change, and as far as I can tell, I do not have any input or output files for mopac, so I don't have anything to change or send.
> 
> On Oct 28, 2010, at 12:17 PM, Scott Brozell wrote:
> > On Thu, Oct 28, 2010 at 10:39:40AM -0600, Andrea L Edwards wrote:
> >> 
> > --------------
> > 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
> > 


More information about the Dock-fans mailing list