Subject: autodock pdbq file

From: "will" <ewlowe*at*helios.acomp.usf.edu>
Date: Mon, 12 Jul 2004 19:43:16 -0400

Thanks to a lot of help from those on this board, I've gotten over many
hurdles I've encountered in trying to use autodock without any linux or
modeling experience.  It seems now that the only problem I have is with
the 'finish work.'  I've gotten all the data my PI requested of me, but
now need to make some docked illustrations for some publications.  All
of my pdbq files used in the dockings however have a problem with
connectivity.  Once saved as a pdbq file, it gets pretty messy.  I've
attached a picture of FAD as an example.  If someone could please help
me in getting around this problem, I would greatly appreciate it.  I
also have downloaded opendx and compiled it on cygwin, but am unable to
compile CTC chemistry extensions for some reason using the cygwin
makefile provided.  I get the following error:
 
Make: *** [bin/addbonds] error 1
 
So, the only program I'll have to depicting my modeling is ViPEr that
came with ADT package and what I can do with PMV.  Anyone with useful
'networks' for ViPEr that care to share, it would be greatly
appreciated.  Also, is it possible to make a 'docking movie' with
ADT/ViPEr?  Thank you for your time
 
Will
ewlowe*at*helios.acomp.usf.edu
university of south florida
department of chemistry and biochemistry