[Dock-fans] Amber/dock run "dock6 -i dock.in" err!

[Scott Brozell]

Hi,

On Thu, 12 Mar 2009, li bai wrote:

> I study the Amber/dock from the website "http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm"
> 
> But when I use the "dock6 -i dock.in", the wrong come on:
> "
> Computing the receptor energy:
>     mm_options:  diel=C
>     mm_options:  gbsa=0
>     mm_options:  nsnb=99999
>     mm_options:  cut=18.0
>     mm_options:  gb=5
>     mm_options:  ntpr=1
>     mm_options:  cut=999.0
>     mm_options:  gbsa=1
> ff:   1  -4584.94   1790.38   1133.44  -5336.92     44.47  -2216.31  4.07e+01
> lig.1
> Reading parm file (1lgu.lig.1.prmtop)
> title:
>                                                                                 
> getpdb: can't open file lig.1.amber.pdb
> "
> what is wrong ? Who can help me?

prepare_amber.pl is a necessary step before docking with Amber score
- correct your previous issue.

Scott