[Chimera-users] Bond change
bruno.cramer at gmail.com
Mon Nov 30 12:38:36 PST 2009
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.
How can this arbitrary bond change be avoided?
Attached zip file with *.mol2 examples of one compound after splitting process.
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