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
--
VIVEK SHARMA
HBG BI
"I never think of the future - it comes soon enough."
A.Einstein