Reply To: Ab Initio Modelling of Protein with Small-Molecule Cofactor

[Anonymous]

Is the protocol adequately initializing the FAD? Could you try a short run without the constraints, and see if an FAD is present in the output file? (That is, are the constraints an issue or just a symptom.) Looking at your input sequence, you may need to include the FAD’s single letter code (“Z”) prior to the brackets. (So that would be “{rest of sequence}KLMPZ[FAD]”.)

As you’re getting a segmentation fault, compiling and running the debug mode, if you’re able to, (compiling without the “mode=release” on the scons command line, and using the resulting “.linuxgccdebug” or equivalent executable) should give better diagnostics of the failure, even without using a debugger – though doing the recompile and debug-mode run can be tediously slow.

(Another thing to double check is that there are atoms of the appropriate name in the centroid topology file and not just the full atom topology file.)