Dear all,
I'm trying using Jligand for generating a new ligand describition. Have to
say I'm using it for the first time, but so far it look very nice.
I trying to optimize a new lib file for a modified NAD molecule.
I'm using a nad_ebi.cif file of NAD supplied by Garib a while ago which
works fine in Refmac.
Now I working on a hydroxylated molecule of NAD (NADOH), OH group at C6N of
the nicotinamid ring of NAD.
what I have done:
starting jligand
importing the nad_ebi.cif file
showing hydrogens
changing atom type and name of H6N to O6N of the nad_ebi.cif file
change the ligand ID to XAD
regularize XAD (ligand > regularize > XAD)
and I am always ending up with a screwed up nicotinamid ring!
the C5N carbon atom is moving out of the aromatic ring.
I tried to change the bond type to aromatic and/or delocated of the
nicotinamid ring but it is always the same result.
Am I doing something very bad here? Please could you advice me how to get it
right??
It is worse when I start with the original NAD dictionary directly within
Jligand !
Please try out for yourself, any help is much appreciated
Many thanks for your help
Stefan
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