How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?
Hello, The Mol2 saving dialog has an option to save all models to "a single file [individual @MOLECULE sections]” <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#mol2> If you are preparing the structures with Dock Prep, the Mol2 saving dialog will automatically appear after the other steps are done. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html> The format needed for DOCK6 is described in the DOCK6 manual. Depending on what DOCK6 options you use, you may need to edit the Mol2 file yourself after Chimera writes it, such as to add SOLVATION or AMBER_SCORE_ID for certain types of scoring, as mentioned in this page: <http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#TriposMOL2Format> If you have questions specifically about DOCK6, the best place to ask is on the dock-fans mailing list: <http://mailman.docking.org/mailman/listinfo/dock-fans> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 22, 2019, at 8:16 PM, prasad ssv <prasad.ssva@gmail.com> wrote:
How do i save all pdb files into a single mol2 file individually..what is the correct format of that mol2 file to proceed for docking in dock6?
hi,
i had sdf file which contain a library of molecules,may be in thousands. and i want to minimize all those compounds for dockig,when i am adding hydrogen it showing some reply log as attached below. could you please help me to sort it out.i would like assign charges also for those molecules and save as mol2 files in single file. thanking you,
Hi Prasad, (I changed the subject line to something more descriptive) First use the Chimera GUI and try using commands on a few example molecules, to figure out what commands you want to use. See command “minimize” with “nogui true” option (which will include adding hydrogens and charges) and command “write” (to save as mol2). Make sure to read the instructions carefully, especially for the “nogui” option of minimize: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html> Then if you need to loop through multiple inputs, you would put the commands into a script. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> Make sure your SDF are 3D molecules. Sometimes SDF files only have flat 2D diagrams that are not suitable for processing with Chimera. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 30, 2019, at 3:23 AM, prasad ssv <prasad.ssva@gmail.com> wrote:
hi, i had sdf file which contain a library of molecules,may be in thousands. and i want to minimize all those compounds for dockig,when i am adding hydrogen it showing some reply log as attached below. could you please help me to sort it out.i would like assign charges also for those molecules and save as mol2 files in single file. thanking you,
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prasad ssv