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Hi,</div>
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I have an NAD coming from a PDB file. When I add H to it, Chimera has issues with the nicotinamide ring. It isn't seeing the ring as aromatic. I've saved the NAD without adding H as a .mol2 file and tried to edit it so that it would be seen by Chimera as
being aromatic, but it is still adding 2 H's to some of the C in the ring that only should one. I've attached the mol2 file that I've edited.
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I've also tried to edit the .mol2 file where I've changed the C in the ring to C.2 and changed the bonds to double bonds (e.g. N1N, atom 36, and C2N, atom 37, have a double bond, C2N also has a single bond to C3N, and C2N is assigned C.2, but when I add H Chimera
still puts two H on C2N).</div>
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I can add the H and then delete the extra ones in Chimera, but then the bond angle for the remaining H is wrong. Ideally, I'd get Chimera to see the system as aromatic. But I'll take any input on the best way to start with a structure like this and get Chimera
to create something that is close to NAD.<br>
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Thanks!</div>
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Peter Palenchar<br>
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