[Chimera-users] Chimera add H to NAD

[Peter Palenchar]

Hi,

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.

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).

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.

Thanks!

Peter Palenchar
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200703/02a67d9f/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NADf1SC6_A_edited.mol2
Type: application/octet-stream
Size: 4410 bytes
Desc: NADf1SC6_A_edited.mol2
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20200703/02a67d9f/attachment.obj>