[Dock-fans] Amber-Score Error

Scott Brozell sbrozell at scripps.edu
Tue Jul 3 10:46:58 PDT 2007


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



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