From burgosgu at ualberta.ca Mon Oct 1 07:39:29 2007 From: burgosgu at ualberta.ca (burgosgu at ualberta.ca) Date: Mon, 01 Oct 2007 08:39:29 -0600 Subject: [Zinc-fans] uploading sets to ZINC Message-ID: <20071001083929.yr6xkqd3ms8oc8s0@webmail.ualberta.ca> Hi everyone, I tried to upload a set to (ZINC http://zinc.docking.org/upload.shtml), but the page says that currenty the resource is broken. Does anybody knows when will it be available? THANKS From jji at cgl.ucsf.edu Tue Oct 2 09:41:07 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 02 Oct 2007 09:41:07 -0700 Subject: [Zinc-fans] uploading sets to ZINC In-Reply-To: <20071001083929.yr6xkqd3ms8oc8s0@webmail.ualberta.ca> References: <20071001083929.yr6xkqd3ms8oc8s0@webmail.ualberta.ca> Message-ID: <470274A3.1060307@cgl.ucsf.edu> Hi - Please try the beta version at http://zinc8.docking.org/upload.shtml John burgosgu at ualberta.ca wrote: > Hi everyone, > > I tried to upload a set to (ZINC > http://zinc.docking.org/upload.shtml), but the page says that currenty > the resource is broken. Does anybody knows when will it be available? > > THANKS > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From jji at cgl.ucsf.edu Tue Oct 2 14:57:50 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Tue, 02 Oct 2007 14:57:50 -0700 Subject: [Zinc-fans] uploading molecules for processing ? In-Reply-To: References: Message-ID: <4702BEDE.6080901@cgl.ucsf.edu> Hi Jeff This is a very old message, but while cleaning out my mailbox, I just wanted you to know that the beta of ZINC now has the upload feature working again. http://zinc8.docking.org/upload.shtml Cheers John Jeffrey Dyason wrote: > Hi, > I've just tried uploading a mol2 file to be processed by Zinc and > everything appears to work and I'm given a job number (#37346) with a link > to click to download the processed file but on clicking it, I get the > following :- "You are in a twisty website of broken documents, all > alike... 404, number 404. 404 call" > Is this a problem with the newer version of Zinc ? I seem to remember it > working on the older version. > > Thanks Jeff. > ----------- > Jeff Dyason e-mail: > J.Dyason at griffith.edu.au > Institute for Glycomics http://www.griffith.edu.au/glycomics > Griffith University (Gold Coast Campus) > PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028 > Queensland 9726 Australia Fax: +61 7 5552 8098 > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > > From elite158 at yahoo.com Sat Oct 20 00:43:41 2007 From: elite158 at yahoo.com (elite 158) Date: Sat, 20 Oct 2007 00:43:41 -0700 (PDT) Subject: [Zinc-fans] wget-ting sdf files Message-ID: <221088.9259.qm@web52505.mail.re2.yahoo.com> Hello all Zinc fans, Is there any way to download the "all-purchasable" subset (#6)? from the following link: http://zinc6.docking.org/subset1/6/ by using any automated dowloaders? I understand that there is a limit of downloading 2 files at a time to reduce the server strain, thought I might not neccessarily need to do the same. I want to automate the whole download process by the weekend. I am working on a windows server and tried to emulate the 'GNU-Wget for windows' application. However, I could only download one sdf.gz at a time. Is there a way to automate the whole process so that I can relax in the weekend? regards, Elite158 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20071020/cbbe2d42/attachment.html From jji at cgl.ucsf.edu Sun Oct 21 15:38:03 2007 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Sun, 21 Oct 2007 15:38:03 -0700 Subject: [Zinc-fans] wget-ting sdf files In-Reply-To: <221088.9259.qm@web52505.mail.re2.yahoo.com> References: <221088.9259.qm@web52505.mail.re2.yahoo.com> Message-ID: <471BD4CB.3000308@cgl.ucsf.edu> Hi Elite158 Thanks for your interest in ZINC, and your query about downloading the database using multiple sequential calls of wget. If you run wget via the c-shell scripts we distribute, then they should run sequentially, and there should be no problem. You can get wget for windows from our website should you need it. http://wget.docking.org/. Most other operating systems have wget built in or make it easy to acquire. Good luck! John elite 158 wrote: > Hello all Zinc fans, > > Is there any way to download the "all-purchasable" subset (#6)? from > the following link: > http://zinc6.docking.org/subset1/6/ by using any automated dowloaders? > I understand that there is a limit of downloading 2 files at a time to > reduce the server strain, thought I might not neccessarily need to do > the same. I want to automate the whole download process by the weekend. > > I am working on a windows server and tried to emulate the 'GNU-Wget > for windows' application. However, I could only download one sdf.gz at > a time. Is there a way to automate the whole process so that I can > relax in the weekend? > > regards, > Elite158 > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com > > ------------------------------------------------------------------------ > > _______________________________________________ > Zinc-fans mailing list > Zinc-fans at docking.org > http://blur.compbio.ucsf.edu/mailman/listinfo/zinc-fans > From burgosgu at ualberta.ca Thu Oct 25 18:13:18 2007 From: burgosgu at ualberta.ca (burgosgu at ualberta.ca) Date: Thu, 25 Oct 2007 19:13:18 -0600 Subject: [Zinc-fans] Fixing protonation state Message-ID: <20071025191318.1vi22p54cow8c48s@webmail.ualberta.ca> Hi everybody, I need to have a compound correctly protonated to dock it. I tried to use the resource of "upload sets" of ZINC, but it seems that it does not have the required charactersitics of bioavailability and non-toxicity, because it gives me no output as it did with other compounds. The smile for this compound is: C1=C(C=CC2=C1C(=C[N]2)CC(=O)NCCCNCCCCNCCCNC(=O)CC3=C[N]C4=C3C=C(C=C4)Br)Br Any suggestions?? THANKS, Asdrubal From letiendzung at yahoo.com Fri Oct 26 16:56:52 2007 From: letiendzung at yahoo.com (Le Tien Dung) Date: Fri, 26 Oct 2007 16:56:52 -0700 (PDT) Subject: [Zinc-fans] Stereo isomer Message-ID: <731454.18052.qm@web51407.mail.re2.yahoo.com> Dear Zinc-fan, I have a question whether ZINC includes all stereo isomers of a compound? For example I am interested in a compound like L-methionine sulfoxide, and we know this compound has 02 forms L-methionine-S-sulfoxide and L- methionine-R-sulfoxide. Thank you for any inputs Dzung __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20071026/37491806/attachment.html