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loop modeling with KIC mode

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loop modeling with KIC mode
#1

Dear all,
I tried KIC mode when I was doing loop modeling and it seemed to be successfully because I got final structures, with lots of warnings and abnormal coordinates in the final pdb. I will paste the warnings , then part of the abnormal coordinates and input files I used at the last. I really appreciate if someone can take a look and give some comments. Thanks in advance!

#######Warnings from the output after I fire the ENTER#######

protocols.looprelax: ===
protocols.looprelax: === Remodel
protocols.looprelax: ===
protocol.loops.LoopMover: ALL_LOOPS:LOOP begin end cut skip_rate extended
protocol.loops.LoopMover: LOOP 1 4 1 0 0
protocol.loops.LoopMover: LOOP 530 624 558 0 0
protocol.loops.LoopMover: LOOP 643 676 649 0 0
protocol.loops.LoopMover:
protocol.loops.LoopMover: SELECTEDLOOPS:LOOP begin end cut skip_rate extended
protocol.loops.LoopMover: LOOP 1 4 1 0 0
protocol.loops.LoopMover: LOOP 530 624 558 0 0
protocol.loops.LoopMover: LOOP 643 676 649 0 0
protocol.loops.LoopMover:
protocol.loops.LoopMover: Building Loop: LOOP 1 4 1 0 0
protocol.loops.LoopMover: Building Loop attempt: 0
protocol.loops.LoopMover: perturb_one_loop_with_KIC: 1 4
protocol.loops.LoopMover: remodel init temp: 2
protocol.loops.LoopMover: remodel final temp: 1
protocol.loops.LoopMover: kinematic initial perturb with start_res: 1 middle res: 2 end_res: 4
protocol.loops.LoopMover: loop rmsd before initial kinematic perturbation:0
protocol.loops.LoopMover: not performing initial kinematic perturbation
protocols.moves.MonteCarlo: MonteCarlo:: last_accepted_score,lowest_score: 30226.3 30226.3
core.conformation.Residue: WARNING: Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: WARNING: ResConnID info stored on residue 0 is now out of date!
core.conformation.Residue: WARNING: Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: WARNING: ResConnID info stored on residue 0 is now out of date!
core.conformation.Residue: WARNING: Residue connection id changed when creating a new residue at seqpos 1
core.conformation.Residue: WARNING: ResConnID info stored on residue 0 is now out of date!

#######Abnormal coordinates in the final pdb(loop starts from residue 530) #######
(Sorry about the format. The first and second loop is OK but the third loop seems to be in a different coordination system. The coordinates for the third loop is almost 20 times than the coordinates in template pdb)
.......
ATOM 3642 N SER 529 31.083 44.505 7.147 1.00 0.00

ATOM 3643 CA SER 529 32.481 44.775 7.524 1.00 0.00
ATOM 3644 C SER 529 33.337 45.154 6.304 1.00 0.00
ATOM 3645 O SER 529 32.805 45.120 5.167 1.00 0.00
ATOM 3646 CB SER 529 33.105 43.559 8.243 1.00 0.00
ATOM 3647 CEN SER 529 33.171 43.046 8.342 1.00 0.00
ATOM 3648 H SER 529 30.883 43.752 6.504 1.00 0.00
ATOM 3649 N ASP 530 995.946 953.015 902.960 1.00 0.00
ATOM 3650 CA ASP 530 962.479 924.587 931.375 1.00 0.00
ATOM 3651 C ASP 530 884.065 942.893 910.427 1.00 0.00
ATOM 3652 O ASP 530 882.972 947.202 906.600 1.00 0.00
ATOM 3653 CB ASP 530 953.139 933.955 952.661 1.00 0.00
ATOM 3654 CEN ASP 530 963.183 924.408 933.668 1.00 0.00
ATOM 3655 H ASP 530 996.599 953.624 903.432 1.00 0.00
ATOM 3656 N ASP 531 967.706 969.994 897.936 1.00 0.00
ATOM 3657 CA ASP 531 978.322 941.050 932.818 1.00 0.00
ATOM 3658 C ASP 531 968.200 962.272 975.362 1.00 0.00
ATOM 3659 O ASP 531 1000.2671005.795 949.044 1.00 0.00
ATOM 3660 CB ASP 531 1040.951 952.354 968.548 1.00 0.00
ATOM 3661 CEN ASP 531 980.385 939.882 932.413 1.00 0.00
ATOM 3662 H ASP 531 968.443 970.526 897.497 1.00 0.00
.......

#######Command before I fire#######
loopmodeling.#### @flags

#######My flags file#######
-database ~/Rosetta/rosetta3.1/rosetta_database/
-loops::input_pdb template.pdb
-loops::loop_file template.loop_file
-loops::frag_sizes 9 3 1
-loops::frag_files aa####_09_05.200_v1_3 aa####_03_05.200_v1_3 none
-out::prefix temp
-loops::remodel perturb_kic
-nstruct 1
-loops::neighbor_dist 6
-loops::vicinity_sampling
-loops::vicinity_degree 5
-loops::kic_max_seglen 12
-loops::remodel_init_temp 2.0
-loops::remodel_final_temp 1.0

When I replace 'perturb_kic' to 'quick_ccd' and also delete the related options for KIC mode, there are no warnings like I pasted before.

Best,
Wenchang

Tue, 2010-03-02 06:05
wenchangyu2008

A) This is a question about Rosetta 3.1 - you should post on the 3.x board, not the ++ board (I don't check this board very often for 3.1 questions...)

B) Did you have density and occupancy for those loops ahead of time (were all backbone atoms present with nonzero occupancy in the PDB)?

Mon, 2010-03-15 08:41
smlewis

Thanks, smlewis.
Yes, -1.00 for those loops and 1.00 for the residues in template.

Fri, 2010-03-19 16:46
wenchangyu2008