Hi Bruno, What version of Chimera are you using? The problem you're reporting was fixed on March 17th of this year so if you use the current production release candidate you shouldn't have this problem. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Nov 30, 2009, at 12:38 PM, Bruno Cramer wrote:
Hi
After getting the conformations as *.sdf (or *.pdb) files with Macromodel (from Shroedinger) and/or Vconf(VeraChem) I use Chimera to add missing H's and add charges with amber 99. After these steps are completed, I split the sdf conformations-file into single *.mol2 files. All works fine except for the last step, that changes a single bond into a double bond in each molecule. I am correcting this manualy opening the *.mol2 file with Texd editors and changing the double bond into single bond the the benzene rings. Opening a chosen conformation from the *.sdf file it looks correct.So, the problem happens during conversion/splitting process.
Question: How can this arbitrary bond change be avoided?
Attached zip file with *.mol2 examples of one compound after splitting process.
Thank you Regards Bruno <ex.zip>_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users