[Dock-fans] Amber-Score Error

Rima Chaudhuri rima.chaudhuri at gmail.com
Tue Jul 3 11:38:16 PDT 2007


Hello,
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!
Any suggestions?
Thanks

Rima

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
>
> Scott
>
>


-- 
-Rima
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