[Dock-fans] about AMSOL7's input file

John Irwin jji at cgl.ucsf.edu
Thu Apr 28 22:29:28 PDT 2005


Hi - here are the 3 scripts you refer to. I hope this is of some use. Our
scripts are written for AMSOL6.5.3. They work in cartesian space not in
internal coordinate (Z-matrix) space. Good luck. John

John J. Irwin http://johnirwin.compbio.ucsf.edu
Adj. Assistant Professor  http://shoichetlab.compbio.ucsf.edu
Pharmaceutical Chemistry, UCSF, 600 16th St, Suite N474E
San Francisco CA 94143-2240 USA; Phone +1 415 514-4127 Fax x4260

Free 3D screening database: http://zinc.docking.org. If you are interested
in new methods of macromolecular crystallography please see the Erice
Crystallography page http://crystalerice.org. Coming soon:
2006: Structure and Function of Large Molecular Assemblies
2007: Engineering of Crystalline Materials Properties
2008: From Molecules to Medicine - Integrating Crystallography (Drug Design)
 

> -----Original Message-----
> From: dock-fans-bounces at docking.org 
> [mailto:dock-fans-bounces at docking.org] On Behalf Of Gaokeng Xiao
> Sent: Thursday, April 28, 2005 7:46 AM
> To: Kim Branson
> Cc: dock-fans
> Subject: Re: Re: [Dock-fans] about AMSOL7's input file
> 
> dear All,
>      There were some attachment files: lig.mol2, lig.dat, 
> lig.out, fort.12, fort.19, fort.20, fort.21 about a amsol's 
> result I ran. I just typed : amsol < lig.dat > lig.out 
>      I donnot know how to extract charges from lig.out to lig.mol2.
>      And the files fort.19 and fort.20 is empty? Why ?
>      Yes,RemoveJunkLines.awk,SeprAmslOut.pl, Get5Colum.awk do 
> miss in the supp. material.
>       
>       
> 
> 	
> 
> ======= 2005-04-28 11:03:40 wrote:=======
> 
> >-----BEGIN PGP SIGNED MESSAGE-----
> >Hash: SHA1
> >
> >Hi all,
> >
> >the following  hard coded scripts are missing from the supp. 
> material.
> >
> >awk -f /hunter/condor/home/bin/RemoveJunkLines.awk $1 > $1.tmp 
> >/hunter/condor/home/bin/SeprAmslOut.pl $1.tmp $1.l $1.c $1.t awk -f 
> >/hunter/condor/home/bin/Get5Colum.awk $1.c > $1.d
> >
> >perhaps you can dig them up or post them john?
> >cheers
> >
> >Kim
> >
> >>
> >Dr Kim Branson
> >Peter Doherty Fellow
> >Protein Structure and Function
> >St Vincents Institute for Medical Research
> >41 Victoria Parade, Fitzroy
> >Victoria 3065, Australia.
> >Phone: +613 9288 2480
> >Fax: +613 94162 676
> >Ph +613 9662 7136
> >kbranson at svi.edu.au
> >kim.branson at gmail.com
> >www.svi.edu.au
> >-----BEGIN PGP SIGNATURE-----
> >Version: GnuPG v1.2.4 (Darwin)
> >
> >iD8DBQFCcFKM3QNu8KNs0LgRAgNgAJ9ZzkICB6anmL0vsDynQgPROJ/K+ACfQpgc
> >vXFjL5iU702uFOAIvxkyyzc=
> >=kEsp
> >-----END PGP SIGNATURE-----
> 
> = = = = = = = = = = = = = = = = = = = =
> 			
> 
>         致
> 礼!
>  
> 				 
>         Gaokeng Xiao
>         gkxiao at people.com.cn
>           2005-04-28
> 
> 
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