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From: Iresh <wgi...@gm...> - 2017-03-12 16:05:55
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Dear Sir/ Madam, I like to know proper installation guidelines of this software on linux. I installed, but still there is a problem that this is a stand alone one or a plugging to the Openbabel software. Thank You, |
From: Paolo T. <pao...@un...> - 2012-04-24 05:49:00
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Dear Bill, you will only need to convert the PDB to SDF with OpenBabel (included in Open3DTOOLS). To include Open3DTOOLS in the path do the following: 1) Under Linux/Mac OS X/other UNIX: $ . /path/to/open3dtools/bin/env_babel.sh 2) Under Windows > C:\path\to\open3dtools\bin\env_babel.bat then $ babel -ipdb protein.pdb -osdf protein.sdf Then in Open3DGRID just: Open3DGRID> import type=sdf file=protein.sdf Open3DGRID> calc_field type=... etc. Please let me know if this works for you. Best regards, Paolo On 04/23/2012 11:01 PM, McLaughlin, William wrote: > > To whom it may concern: > > I would like to see how the open3Dgrid can be run on protein > structures. Please let me know how to possibly use the program with > pdb formatted files. > > Sincerely, > > Bill McLaughlin > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > > _______________________________________________ > Open3dgrid-discuss mailing list > Ope...@li... > https://lists.sourceforge.net/lists/listinfo/open3dgrid-discuss -- ========================================================== Paolo Tosco, Ph.D. Phone: +39 011 6707680 Department of Drug Science Fax: +39 011 6707687 and Technology Mob: +39 348 5537206 Via Pietro Giuria, 9 10125 Torino, Italy http://open3dalign.org E-mail: pao...@un... http://open3dqsar.org ========================================================== |
From: McLaughlin, W. <wmc...@tc...> - 2012-04-23 21:40:53
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To whom it may concern: I would like to see how the open3Dgrid can be run on protein structures. Please let me know how to possibly use the program with pdb formatted files. Sincerely, Bill McLaughlin |
From: <cas...@uf...> - 2011-05-30 14:56:55
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Dear Open3dGrid users, I have just installed Open3Dgrid and I am anxious to see its capability, but my programming skills are limited. As a consequence there some issues that I would like to clarify: 1) Is there a sample script that can be used to test Open3Dgrid with macromolecules ? 2) Which input format should I use (mol2, pdb)? 3)How do I use pymol to set Open3Dgrid parameters? Yours, Marcelo ---------------------------------------------------------------- Universidade Federal da Bahia - http://www.portal.ufba.br |