Dear sir,

Please have a look to this error. I made a normal modeller run (7v7) to generate 50 structures for a target sequence of about 500 residues using 3 different templates. But after generating 6 intial structure, it died with this following details, this log file was pretty big in size and contained this detail.

I regularly use MODELER , but this a new kind of error I faced, what can be the reason?

---------------------- 25 Phi/Psi pair of dihedral restraints : 1.0000 26 Distance restraints 4 (SDCH-SDCH) : 1.0000 27 Distance restraints 5 (X-Y) : 1.0000 28 NMR distance restraints 6 (X-Y) : 1.0000 29 NMR distance restraints 7 (X-Y) : 1.0000 30 Minimal distance restraints : 1.0000 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 34 Absolute position restraints : 1.0000 35 Dihedral angle difference restraints : 1.0000 Initial value of energy before optimization : ---------------- Current energy : ???????????????? Symmetry term within energy : 0.0000 Number of iterations : 200 Number of calls to energy function : 0 Number of updates of dynamic contacts : 5 Number of non-updates of dynamic contacts : 196 Final maximal atomic shift : ???????? TEMPERATURE : 150.000 EQUILIBRATE : 20 EQUILIBRATE : T Seed for the random number generator (RAND_SEED) : 1 Molecular dynamics time step (MD_TIME_STEP) : 4.000 CAP_ATOM_SHIFT : 0.390 Maximal energy, step : ---------------- 0 Minimal energy, step : ???????????????? 200 Average energy, stand.dev. : ???????????????????????????????? Average atomic shift along one axis : ???????? MODEL returned : FINAL

------before this whole log file was filled up with this;

-------------- ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ??????????????? ddihedr_W> central bond too short: ???????????????

---------------

looks like some bond/bonds has gone too short and that might have affected the energy of system to go out of limits. But how can I found out which bond is that or some details like that?

Hoping for a quick reply,

Best regards,

Vivek