User c20bfefb82
09-05-2010 13:53:56
I have just started using Marvin Sketch so my problem is most likely my ignorance. I have tried to draw a compound (N-[(1S)-1-cyano-2-(5-cyano-2-trifluoromethyl-phenoxy)-1-methyl-ethyl]-4-trifluoromethylsulfanyl-benzamide) by hand and by importing from the IUPAC name and found the process extremely easy. My problem comes when I try to save the structure as a pdb (mol, mol2 or even mrv) file. Reopening the structure shows that all the double and triple bonds have disappeared including the aromatic rings and a new double bond appears between the aromatic ring and sulphur atom. Where on earth am I going wrong?
Mac 10.6.3
Marvin Sketch 5.3.2
User c20bfefb82
10-05-2010 01:53:17
Answered my own question eventually. After some reading between the lines it seems that the bonding between atoms is determined from the distance between atoms in a pdb, even though the pdb file specifies CONECT data between different atoms. If you draw a structure in Marvin Sketch and just save it as pdb, the atoms are not the right distances apart. If you use the Conformer tool to find the conformation with the minimum energy then the atoms will be spaced correctly. Saving this conformer to a pdb file can be re-opened and tho bonding configuration shows up correctly. Rookie mistake but I thought the answer might be useful to someone.
ChemAxon 990acf0dec
13-05-2010 07:24:18