On 09/01/12 06:13, Shveta Bisht wrote:
I need advise on the way I have run prodrg and the explanations for the results.
There is little room for manoeuvre when running prodrg.
Prodrg is not the Font of All Ligand Wisdom.
Prodrg makes mistakes.
If you think that the bond lengths are wrong, change them.
You can use CCDC's Mogul to assist in the restraints manipulation.
Is it common to observe such values? Or it is due to the alternating single and
double bonds in this structure.
You can test this yourself by generating different but related ligands.
You might like to use the CCP4 version rather than the web version which
it seems that you are currently using.
Other restraints-generating software is available.
HTH,
Paul.
