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
