I'm trying to simulate various length of polyproline using the itasser suite.
The simulations completed, but with some of the following warnings about blast results and hydrogen bonds (see below). Given what is already known about polyproline, I would have expected it to spontaneously form defined helices which is known in the literature, stabilised via hydrogen bonds. However when I view the models in UCSF Chimera (which attempts to assign secondary structure to a molecule upon loading using KSdssp). I see them as semi-helical random coil.
Are there some parameters I could maybe optimise to tweak the output I'm getting - or any general advice would be appreciated.
Your setting for running I-TASSER is:
-pkgdir = /home/ubuntu/Applications/itasser
-libdir = /home/ubuntu/Applications/itasser/itlib
-java_home = /usr/
-seqname = polyproline50
-datadir = /home/ubuntu/polyproline/polyproline50
-outdir = /home/ubuntu/polyproline/polyproline50
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false
1. make seq.txt and rmsinp
Your protein contains 50 residues:
> polyproline50
PPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPPP
2.1 run Psi-blast
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
FORTRAN STOP
30000 6379375 total lib str & residues
number of observations 45.79853 343489.0
pair done
3.1 do threading
start serial threading PPAS
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/PPAS_polyproline50
hostname: protein-simulation-2
starting time: Wed Oct 26 20:44:41 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running zalign .....
ending time: Wed Oct 26 20:50:56 UTC 2016
start serial threading dPPAS
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/dPPAS_polyproline50
hostname: protein-simulation-2
starting time: Wed Oct 26 20:50:58 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running zalign .....
ending time: Wed Oct 26 20:57:19 UTC 2016
start serial threading dPPAS2
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/dPPAS2_polyproline50
hostname: protein-simulation-2
starting time: Wed Oct 26 20:57:21 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running zalign .....
ending time: Wed Oct 26 21:03:40 UTC 2016
start serial threading Env-PPAS
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/Env-PPAS_polyproline50
Illegal division by zero at /home/ubuntu/polyproline/polyproline50/Env-PPAS_polyproline50 line 355.
hostname: protein-simulation-2
starting time: Wed Oct 26 21:03:42 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running zalign .....
start serial threading MUSTER
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/MUSTER_polyproline50
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
hostname: protein-simulation-2
starting time: Wed Oct 26 21:10:16 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running Psi-blast .....
running zalign .....
==>1nayA 2miiA 15.0961172776773 11.6640497613688
1nayA 2miiA 40 32
score_flag=1
ending time: Wed Oct 26 21:25:59 UTC 2016
start serial threading wPPAS
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/wPPAS_polyproline50
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
hostname: protein-simulation-2
starting time: Wed Oct 26 21:26:01 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running Psi-blast .....
ending time: Wed Oct 26 21:40:41 UTC 2016
start serial threading wdPPAS
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/wdPPAS_polyproline50
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
hostname: protein-simulation-2
starting time: Wed Oct 26 21:40:43 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running Psi-blast .....
ending time: Wed Oct 26 22:01:29 UTC 2016
start serial threading wMUSTER
/tmp/ubuntu/ITpolyproline50
/home/ubuntu/polyproline/polyproline50/wMUSTER_polyproline50
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
hostname: protein-simulation-2
starting time: Wed Oct 26 22:01:30 UTC 2016
pwd: /tmp/ubuntu/ITpolyproline50
running Psi-blast .....
running Psi-blast .....
==>1nayA 2miiA 16.0698774094406 14.567298484477
1nayA 2miiA 40.00 32.00
score_flag=1
ending time: Wed Oct 26 22:33:02 UTC 2016
3.2 make restraints
without init: /home/ubuntu/polyproline/polyproline50/init.Env-PPAS
type= easy, n_good=35, M0= 7, M1_for_medm=1.4, n_sg= 7 role=SEQ
domain2=no
type=easy----n_temp_use_for_restraints=20
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
run simulation job 2 / 14
run simulation job 3 / 14
run simulation job 4 / 14
run simulation job 5 / 14
run simulation job 6 / 14
run simulation job 7 / 14
run simulation job 8 / 14
run simulation job 9 / 14
run simulation job 10 / 14
run simulation job 11 / 14
run simulation job 12 / 14
run simulation job 13 / 14
run simulation job 14 / 14
5.1 do clustering
No. of trajectory files: 62
8.000000 3.500000 12.00000
5.2 build full-atomic model
6 Estimate local accuracy of models and B-factor
No hydrogen bonds found in model_tmp.pdb
No hydrogen bonds found in model_tmp.pdb
No hydrogen bonds found in model_tmp.pdb
No hydrogen bonds found in model_tmp.pdb
No hydrogen bonds found in model_tmp.pdb