Thanks for the tip! This is working well for me. Another thing I want to know. Well I need to filter my data gor virtual screening. As we don't have much computation resources for going with large number of molecules, so we decided to go with similarity search first then with structure based docking. So how much this will be reliable and will it be a good starting point? Thank you
On Sun, 29 Dec, 2019, 11:59 Craig James, <cja...@emolecules.com> wrote: > > > On Fri, Dec 27, 2019 at 7:48 AM suyash pant <suyashni...@gmail.com> wrote: > >> Hello sir/mam >> I hope You are doing well >> I am writing this mail, as I am facing certain problem with doing the >> similarity search using "Openbable" >> I have a zinc dataset for lead like and drug like molecules. >> Unfortunately I am not able to go with structure based docking for the >> complete dataset. Similar like zinc dataset I have some more dataset and I >> want to further proceed with tanimoto similarity search first to filter and >> reduce the dataset for my virtual screening and docking. >> Now here when I am taking my reference structure (smilies) for similarity >> search using command *"babel mymols.fs results.sdf >> -sCC1=CC=C(C=C1)C2=C(C=C(C=C2)F)COC3=CC=C(C=C3)CCC(=O)O -at0.6"* So I >> want why I am getting a syntex error and when I am taking same smilie code >> mentioned in your website it is giving. Is there any problem with my smilie >> code or I am doing something wrong? >> > > I assume you are using Linux or a Unix-like operating system such as a > Macintosh. In that case, you must use quotes around the SMILES, because it > contains special characters that the command-line shell tries to interpret. > Try this command with the quotes exactly as shown: > > babel mymols.fs results.sdf > -s"CC1=CC=C(C=C1)C2=C(C=C(C=C2)F)COC3=CC=C(C=C3)CCC(=O)O" -at0.6 > > > Craig > > > Kindly, provide the needful assistance for the mentioned issue. >> Thank You >> >> Suyash Pant >> Research Scholar, >> NIPER, Kolkata >> Department of Pharmacoinformatics >> _______________________________________________ >> OpenBabel-discuss mailing list >> OpenBabel-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> > > >
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
