[Dock-fans] DOCK error in prepare_amber.pl

snoze pa snoze.pa at gmail.com
Fri Feb 1 14:29:12 PST 2008


I am following this tutorial

http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm


But I am unable to get the file lig.1.amber.pdb

Here is my log

perl prepare_amber.pl lig.mol2 1lgu.pdb
Coordinate and parameter files for the Receptor 1lgu generated.
The AMBER score tagged mol2 file lig.amber_score.mol2 generated.
Splitting the multiple Ligand mol2 file into single mol2 files.
The single mol2 files will have the prefix: lig
Generating coordinate and parameter files with AM1-BCC charges.
This may be time consuming.
Ligand lig.1 has total charge 0
Coordinate and parameter files for the Ligand lig.1 generated.
Coordinate and parameter files for the Complex 1lgu.lig.1 generated.
prepare_amber.pl completed.

and when i am running dock then it is unable to find the file
Initializing Library File Routines...
getpdb: can't open file lig.1.amber.pdb


Any Help

Thanks in advance
s
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