[Dock-fans] ligand file input

BRILLET Loraine 216515 loraine.brillet at cea.fr
Mon Jul 16 00:18:39 PDT 2007

Dear all,


I have noticed that the Tripos mol2 atom/bond types given to ligands
when converting them to mol2 format depend on the program used to do
that. For example, I used Chimera and OpenBabel to prepare the mol2 file
for nocodazole (adding H and partial charges). You can see that the
atom/bond types are different (see files included).

Do these different atom/bond types have an influence on the docking
results with DOCK?




Loraine Brillet




-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment.html 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: nocodazole_chimera.mol2
Type: application/octet-stream
Size: 3334 bytes
Desc: nocodazole_chimera.mol2
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment.obj 
-------------- next part --------------
A non-text attachment was scrubbed...
Name: nocodazole_openbabel.mol2
Type: application/octet-stream
Size: 3373 bytes
Desc: nocodazole_openbabel.mol2
Url : http://blur.compbio.ucsf.edu/pipermail/dock-fans/attachments/20070716/8f978deb/attachment-0001.obj 

More information about the Dock-fans mailing list