[Dock-fans] Amber-Score Error

Scott Brozell sbrozell at scripps.edu
Tue Jul 3 12:00:03 PDT 2007


Hi,

On Tue, 3 Jul 2007, Rima Chaudhuri wrote:

> I changed the names of bondtype.mpi  and atomtype.mpi to bondtype and
> atomtype, and now that part works but the amberize ligand now gives the
> following
>
> Running: $AMBERHOME/bin/divcon
> sh: /n1/nprog/amber/amber9/bin/divcon: cannot execute
> Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly,
> exit
> Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> Running: /n4/rima_temp/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> ANTECHAMBER_AC.AC -p gaff
> Cannot open file ligand_all.2.gaff.mol2, exit
>
> I checked, the divcon file is in the mentioned directory!

Not sure what your last sentence means: does
/n1/nprog/amber/amber9/bin/divcon
exist and is it executable ?

Anyway, this is a known problem with antechamber;
the solution is to undefine AMBERHOME.
Then the DOCK executables will be used.

Scott

> On 7/3/07, Scott Brozell <sbrozell at scripps.edu> wrote:
> >
> > Hi,
> >
> > On Tue, 3 Jul 2007, Rima Chaudhuri wrote:
> >
> > > I am trying to rescore a set of 30 molecules using Amber Score of
> > version
> > > dock6.1 parallel on a sgi machine. I applied the bugfix2.
> > > Post prepare_amber.pl I get the desired files except the lig.1.amber.pdb
> > ,
> > > lig.1.gaff.mol2 and  lig.1.frcmod files for each of the ligands.
> > > The script gets me all the required receptor files and complex
> > files(which I
> > > doubt is correct, since the ligand files were not written properly).
> > > On further investigation I see in the amberize_ligand.1.out file :
> > >
> > > running: antechamber to generate GAFF mol2 file format with AM1-BCC
> > charges
> > > sh: /n4/rima_temp/dock6/bin/bondtype:  not found
> > > Error: cannot run "/n4/rima_temp/dock6/bin/bondtype -i
> > > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
> > > judgebondtype() of antechamber.c properly, exit
> > > Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0
> > -o
> > > ANTECHAMBER_BOND_TYPE.AC -f ac -j full
> > > Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit
> > >  ...
> > >  ...
> > >  ...
> > > AMBER General Force Field for organic mol., add. info. at the end (June,
> > > 2003)
> > > Could not open file flex_GRL_charge_ranked.29.frcmod: not found
> > > Could not open file flex_GRL_charge_ranked.29.gaff.mol2: not found
> > >
> > >
> > > As a result, it cannot write/read the frcmod and gaff.mol2 files for the
> > > ligand.
> > > In my dock6/bin directory, the bondtype is bondtype.mpi , also atomtype
> > is
> > > atomtype.mpi etc..I tried to look into the amberize_ligand script to see
> > > where I could change the 'bondtype' to 'bondtype.mpi' but could not find
> > > so...can someone tell me where is the code/codes that needs to be
> > changed?
> > > or what should I be doing now?
> > >
> > > P.S: I changed some names for e.g. antechamber to antechamber.mpi and
> > > parmchk to parmchk.mpi and teLeap to teLeap.mpi etc ...
> >
> > Apparently, the mpi suffix is being applied to all executables,
> > not just parallel ones.  A workaround is to build serially:
> >
> > cd install
> > make distclean
> > ./configure sgi
> > make install
> > make test
> >


More information about the Dock-fans mailing list