[Dock-fans] Amber-Score Error

Rima Chaudhuri rima.chaudhuri at gmail.com
Tue Jul 3 10:15:53 PDT 2007

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
judgebondtype() of antechamber.c properly, exit
Running: /n4/rima_temp/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
Cannot open file flex_GRL_charge_ranked.29.gaff.mol2, exit
AMBER General Force Field for organic mol., add. info. at the end (June,
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
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 ...

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