Larry Grant wrote:
I am attempting to fit NAD to a 2.1 A lactate dehydrogenase structure
I've built and I'm running into several problems:
1. I loaded NAD from the COOT monomer library and was able to fit
roughly 2/3 of it into the density using the real space refine zone
function but the nicotinamide moiety flies apart as a result of the
refinement. My work around for this was to load another ligand and
roughly fit just the nicotinamide ring then cut and paste the
coordinates from the second ligand into the file for the first. I then
merged the ligand with the LDH structure using the merge molecules
function in COOT. I fit NAD to four different chains this way.
Attempting to refine the ligands after merging also results in the
ring coming apart.
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0905&L=COOT&P=R6200&1=COOT&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4
2. I was hoping that a round of refmac would then refine the entire
ligand and thereby neatly fit the crudely placed nicotinamide ring.
When I run refmac it fits the first NAD fairly rigidly such that while
it does fit the nicotinamide ring it knocks the adenine moiety out of
place. The other three NAD's look like they imploded. The atoms are
too close together resulting in a structure which looks nothing like
NAD and which contains multiple carbons with greater than four bonds.
I was advised to create a new ligand dictionary and attempt refmac
refinement with it.
That should not be necessary.
I have created files using refmac in review mode, loading the NAD
coordinates into Sketcher and running libcheck, the PRODRG server and
downloading from the HIC-UP server. Running refmac with any of these
libraries produces the exact same result.
The devil's in the detail.
Trying to use the real space refine zone on the one ligand which
didn't come apart gives me the error message "No Restraints Found!".
If you are talking about Coot, then you need to make sure that the new
dictionary you read in matches the comp_id of the residue/monomer you
are trying to refine.
Paul.
