From cpsosa at msi.umn.edu Mon Sep 15 11:45:54 2008 From: cpsosa at msi.umn.edu (Carlos P Sosa) Date: Mon, 15 Sep 2008 13:45:54 -0500 (CDT) Subject: [Dockdev] ZINC structures question Message-ID: <9dba34438fdfbd1ea1c700b4d8d43673.squirrel@www.msi.umn.edu> Hello, According to the official ZINC paper, the structures defined in ZINC come from "suppliers as 2D SDF files". How accurate are these structures compared to experiment? When adding new groups to this structures, what is the recommended way to do it? via QM calcs? Thanks, From jji at cgl.ucsf.edu Mon Sep 15 12:06:05 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Mon, 15 Sep 2008 12:06:05 -0700 Subject: [Dockdev] ZINC structures question In-Reply-To: <9dba34438fdfbd1ea1c700b4d8d43673.squirrel@www.msi.umn.edu> References: <9dba34438fdfbd1ea1c700b4d8d43673.squirrel@www.msi.umn.edu> Message-ID: <48CEB21D.4040506@cgl.ucsf.edu> Hi Carlos Thanks for your email. Carlos P Sosa wrote: > Hello, > > According to the official ZINC paper, the structures defined in ZINC come > from "suppliers as 2D SDF files". How accurate are these structures > compared to experiment? Catalogs aren't accurate at all, they are just depictions of molecules in 2D. Thus they aren't "real structures" at all. > When adding new groups to this structures, what > is the recommended way to do it? via QM calcs? > The structures in ZINC are processed using Corina to make 3D models, and ligprep, to generate biologically relevant tautomers and protonation states. I understand your question to mean, if you wanted to chemically derivatize structures in ZINC, how should it be done? If that is right, I would say it depends on the application. But for simply generating "reasonable 3D structures for modeling" I would consider making the change in 3D, and then going back to SMILES, and regenerating the structure using Corina or other similar SMILES to 3D tools. Of course, you can use QM calculations to refine the geometry of any 3D structure. However, this would normally be a gas-phase structure, at a single conformation, so you'll still need to sample its structure in the binding site, perhaps using QM calcs to refine the docking pose. If I misunderstood, please feel free to ask again. John UCSF ZINC Team From cpsosa at msi.umn.edu Thu Sep 18 09:04:39 2008 From: cpsosa at msi.umn.edu (Carlos P Sosa) Date: Thu, 18 Sep 2008 11:04:39 -0500 (CDT) Subject: [Dockdev] printing conformers Message-ID: <5bd74a05e09a3eb9990388312a0265eb.squirrel@www.msi.umn.edu> Hello Developers, I would like to print all the different conformers that DOCK6 scored and not just the final structure. To try to accomplish that, I am looking at: num_scored_conformers_written 1 but I could not find this documented in the 6.2 manual. What number should I change it to? Thanks, p.s. More information, what I would like to do is to print all the different poses that DOCK6 tested with the grid-based scoring function. A history of structures before it found the final pose. From cpsosa at msi.umn.edu Thu Sep 18 11:59:32 2008 From: cpsosa at msi.umn.edu (Carlos P Sosa) Date: Thu, 18 Sep 2008 13:59:32 -0500 (CDT) Subject: [Dockdev] write_orientations Message-ID: <1798b90a7e49b58b525a7be27197d97c.squirrel@www.msi.umn.edu> Hello Developers, Activating these two flags create a mol2 file with only info. about the anchor. Is there a way to get anchor plus more layers? write_orientations no num_scored_conformers_written 1 Thanks, From sbrozell at scripps.edu Thu Sep 18 14:53:42 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 18 Sep 2008 14:53:42 -0700 (PDT) Subject: [Dockdev] printing conformers In-Reply-To: <5bd74a05e09a3eb9990388312a0265eb.squirrel@www.msi.umn.edu> Message-ID: Hi, My preference is to send these operational questions to dock-fans in the hope that someone besides John or me will answer them. By the way, I invite comments on ways to foster more user participation on answering dock-fans. If it aint in the manual then it dont exist :+-O http://dock.compbio.ucsf.edu/DOCK_6/new_in_6.2.txt Previously, the parameter num_scored_conformers_written controlled both the number of conformations scored by the primary scoring function, as well as the number of conformations written. In the new release, these two functions have been decoupled into two user parameters: num_scored_conformers, which sets the number of conformations to be scored by the primary scoring function, and write_conformations, which controls whether these conformations will be written. Of course, on dock-fans I cannot be such a smart aleck. ;-) Scott On Thu, 18 Sep 2008, Carlos P Sosa wrote: > I would like to print all the different conformers that DOCK6 scored and > not just the final structure. To try to accomplish that, I am looking at: > > num_scored_conformers_written 1 > > but I could not find this documented in the 6.2 manual. What number > should I change it to? > > Thanks, > > p.s. More information, what I would like to do is to print all the > different poses that DOCK6 tested with the grid-based scoring function. A > history of structures before it found the final pose. From jji at cgl.ucsf.edu Thu Sep 18 16:36:56 2008 From: jji at cgl.ucsf.edu (John J. Irwin) Date: Thu, 18 Sep 2008 16:36:56 -0700 Subject: [Dockdev] printing conformers In-Reply-To: References: Message-ID: <48D2E618.2020001@cgl.ucsf.edu> > Of course, on dock-fans I cannot be such a smart aleck. > ;-) > Scott > There are 96 of us on dockdev, 432 on dock-fans, 220 on zinc-fans. oh, and hi to you guys from NSA that don't bother to register ;-) From sbrozell at scripps.edu Thu Sep 18 15:14:48 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 18 Sep 2008 15:14:48 -0700 (PDT) Subject: [Dockdev] write_orientations In-Reply-To: <1798b90a7e49b58b525a7be27197d97c.squirrel@www.msi.umn.edu> Message-ID: Hi, My preference is to send these operational questions to dock-fans in the hope that someone besides John or me will answer them. By the way, I invite comments on ways to foster more user participation on answering dock-fans. ECho, Echo, echo. I recall conversations with Terry, where writing growth was discussed; I think the concensus was that this would just blow up in the hands of users due to the multiplicative file size growth. But I think she did emit such info during her pruning algorithm studies. You should seek out the great east bay oracle (and follow up with a summary here). Ok, so this one might have a development aspect. Scott Where does a pirate dock his ship ? In an AARRRRRRRRbor :) On Thu, 18 Sep 2008, Carlos P Sosa wrote: > Activating these two flags create a mol2 file with only info. about the > anchor. Is there a way to get anchor plus more layers? > > write_orientations no > num_scored_conformers_written 1 > From sbrozell at scripps.edu Thu Sep 18 15:24:40 2008 From: sbrozell at scripps.edu (Scott Brozell) Date: Thu, 18 Sep 2008 15:24:40 -0700 (PDT) Subject: [Dockdev] printing conformers In-Reply-To: <48D2E618.2020001@cgl.ucsf.edu> Message-ID: Hi, On Thu, 18 Sep 2008, John J. Irwin wrote: > > > Of course, on dock-fans I cannot be such a smart aleck. > > ;-) > > Scott > > > There are 96 of us on dockdev, 432 on dock-fans, 220 on zinc-fans. oh, > and hi to you guys from NSA that don't bother to register ;-) Hmmm 96 developers; what are their contributions ? Scott From cpsosa at us.ibm.com Thu Sep 18 19:17:40 2008 From: cpsosa at us.ibm.com (Carlos P Sosa) Date: Thu, 18 Sep 2008 21:17:40 -0500 Subject: [Dockdev] write_orientations In-Reply-To: References: <1798b90a7e49b58b525a7be27197d97c.squirrel@www.msi.umn.edu> Message-ID: Per John's suggestion I am using this list, I am certainly willing to use any of these lists and contribute if I can. Also related to conformers, Terry was kind enough to put together a small movie for us but never got info. how to generate the full ligands for a movie that shows the process of docking using DOCK6. Any comments on this matter would also be appreciated. I think that "if" enough info. is provided and not used as a default, most users are going to stay away from such a verbose option. However, once you know what you'll get this info. is very useful. Just by looking at the final anchor selected for growth, you immediately see why in some cases the wrong pose is predicted. From: Scott Brozell To: Carlos P Sosa Cc: Dockdev at docking.org Date: 09/18/2008 06:38 PM Subject: Re: [Dockdev] write_orientations Hi, My preference is to send these operational questions to dock-fans in the hope that someone besides John or me will answer them. By the way, I invite comments on ways to foster more user participation on answering dock-fans. ECho, Echo, echo. I recall conversations with Terry, where writing growth was discussed; I think the concensus was that this would just blow up in the hands of users due to the multiplicative file size growth. But I think she did emit such info during her pruning algorithm studies. You should seek out the great east bay oracle (and follow up with a summary here). Ok, so this one might have a development aspect. Scott Where does a pirate dock his ship ? In an AARRRRRRRRbor :) On Thu, 18 Sep 2008, Carlos P Sosa wrote: > Activating these two flags create a mol2 file with only info. about the > anchor. Is there a way to get anchor plus more layers? > > write_orientations no > num_scored_conformers_written 1 > _______________________________________________ Dockdev mailing list Dockdev at docking.org http://blur.compbio.ucsf.edu/mailman/listinfo/dockdev -------------- next part -------------- An HTML attachment was scrubbed... URL: http://blur.compbio.ucsf.edu/pipermail/dockdev/attachments/20080918/02e838f5/attachment.html