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PostPosted: Tue Oct 01, 2013 9:16 am 
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Joined: Tue Oct 01, 2013 9:08 am
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I'm trying to dock NAD+ to a protein (pubchemID 5893.sdf), which is NAD+, I use babel to convert it to a pdb, then use prepare_lygand4.py and what comes out appears to be NADH. Is there anyway to stop this? I've tried all of the options available, but always get the same result. Any ideas how to keep NAD+?

Attachments: the files in question.


Attachments:
File comment: Output file (bonds rearranged)
5893.pdbqt [5.82 KiB]
Downloaded 256 times
File comment: Original file.
5893.sdf [9.07 KiB]
Downloaded 241 times
File comment: Second file (converted by babel)
5893.pdb [11.65 KiB]
Downloaded 244 times
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