Hello langren, Please attach the SDF in your email to the mailing list. Please also attach the resulting PDB file, and explain what the correct PDB file should contain.
This will help us find the problem. Regards, Noel 2009/10/12 langren <[email protected]>: > Dear there, > I am currently working on molecular docking of a particular ligand, > phenethyl isothiocyanate. The SDF file can be found in ChemBank, and what I > need to do is simply to change the file into PDB file. But when > the conversion was done, I found all the double bonds (in benzole or S=C=N-) > were missing. I have no idea what is going on, and how should I deal with > that. > Thanks in advance. > > The SDF code is shown below > > 1049672 > SMI2MOL > 11 11 0 0 0 0 0 0 0 0999 V2000 > -3.0700 2.5700 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 > -2.1900 2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > -1.3100 1.5500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 > -0.4300 2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 0.4500 1.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3300 2.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.1800 1.5300 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.0600 2.0400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 3.0700 3.0500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 2.2000 3.5600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1.3300 3.0600 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 > 1 2 2 0 0 0 0 > 2 3 2 0 0 0 0 > 3 4 1 0 0 0 0 > 4 5 1 0 0 0 0 > 5 6 1 0 0 0 0 > 6 11 2 0 0 0 0 > 6 7 1 0 0 0 0 > 7 8 2 0 0 0 0 > 8 9 1 0 0 0 0 > 9 10 2 0 0 0 0 > 10 11 1 0 0 0 0 > M END >> <ChembankId> > 1049672 >> <SMILES> > S=C=NCCc1ccccc1 >> <InChI> > 1/C9H9NS/c11-8-10-7-6-9-4-2-1-3-5-9/h1-5H,6-7H2 > $$$$ > > > > > ________________________________ > 聊天+搜索+邮箱 想要轻松出游,手机MSN帮你搞定! 立刻下载！ > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart your > developing skills, take BlackBerry mobile applications to market and stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
