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

Scott Brozell sbrozell at rci.rutgers.edu
Fri Oct 29 19:55:30 PDT 2010


Hi,

It works for me on the mac below.
Try this:
cd dock6/install/test/amber_score_181l
make clean
make

Is there a file named lig.1.mopac.out ?

scott

% system_profiler SPSoftwareDataType

Software:

    System Software Overview:

      System Version: Mac OS X 10.4.11 (8S165)
      Kernel Version: Darwin 8.11.0
      Boot Volume: Untitled
      Computer Name: pascal’s Power Mac G5


On Fri, Oct 29, 2010 at 01:20:36PM -0600, Andrea L Edwards wrote:
> mac os x 10.6.4 64-bit processor.
> 
> On Oct 29, 2010, at 1:49 AM, Scott Brozell wrote:
> > What are your system details: os, etc ?
> > 
> > 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
> >>> 


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