Synplify will automatically generate constraints for the design in a ".ncf" file while synthesizing. In some instances, the design is overly constrained than expected. How do I prevent ".ncf" generated by Synplify from being read in by NGDBuild?
While invoking Synplify from ISE, right-click on Synthesize in the Processes tab, select "Properties", uncheck "Auto Constrain" and "Write Vendor Constraint File". This will prevent the ".ncf" from being written.
If you use Synplify standalone and create a project in ISE with the ".edf" file, the NGDBuild will automatically find and pick up the ".ncf", as long as the two files are in the same directory and their names are the same. So, if you do not expect the tool to pick up ".ncf", put them in different directories or delete the ".ncf" directly.