[Dock-fans] Problems with prepare_amber.pl

[Francesco Pietra]

I am facing a problem with

prepare_amber.pl  flex_scored.mol2  receptor.pdb

both with the receptor.pdb of previous thread (LEU as first residue;
now this receptor.pdb file comes out correctly using ambodb of Amber9)
and with receptor.pdb files of previous proteins, where prepare..
worked nicely

I had commented out AMBERHOME and its PATH in order to use mopac and
antechamber executables from DOCK6.2 installation. Using the
executables from Amber, same error.

The error (in amberize_complex1.out is: flex_scored.1.gaff.mol2 does
not exist). The only files generated are:

amberize_complex.1.out
amberize_ligand.1.out
amberize_receptor.out
divcon.in
flex_scored.1.log
flex_scored.1.mol2
flex_scored.amber_score.mol2
receptor.amber.pdb
receptor.amber.inpcr
receptor.amber.log
receptor.amber.prmtop

Thus lacking the expected:

flex_scored.1.frcmod
flex_scored.1.gaff.mol2
flex_scored.mopac.out
flex_scored.prmtop
receptor.flex.scored.1.amber.pdb
receptor.flex.scored.1.inpcrd
receptor.flex.scored.1.log
receptor.flex.scored.1.prmtop

i.e., from gaff down, nothing. However:

$ which mopac
/usr/local/dock6/bin/mopac


and all other executables are present in this directory and are on the
path; can be found with "which" from the directory where I am working
in my home. Must be a silly mistake from my side, but as for now I am
unable to remedy.

Thanks for help

francesco pietra