I-TASSER: Change default number (14) of independent runs

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vitamin
Posts: 4
Joined: Fri Apr 30, 2021 3:00 pm

I-TASSER: Change default number (14) of independent runs

Post by vitamin »

Dear developers and community!

See README.txt of installation files:
"I-TASSER structure assembly simulations contains 14 independent
runs by default. This number can be modified if the user wants to run
more simulations, especially for big protein without good templates."

How can I set this parameter to e.g. 20?


Thank you!
robpearc
Posts: 11
Joined: Sun May 02, 2021 5:49 pm

Re: I-TASSER: Change default number (14) of independent runs

Post by robpearc »

Hello,

There is currently no command line option for modifying the number of simulation trajectories. However, these parameters can be modified by changing the parameters in the runI-TASSER.pl file between lines 1613-1629 in the "decide number of runs section", so it will require some more in depth knowledge of the program. On these lines, you can directly change the number of "A" and "M" simulations that will be performed, where "A" stands for the ab initio runs, and "M" is a mixture between ab initio and template-based folding. On these lines, you can see that depending on the target type, different numbers of "A" and "M" trajectories will be run. For example, if the target is an easy threading target, meaning good templates were identified from the PDB, then the simulations will stick closer to the template structures and 10 "M" trajectories will be run alongside only 4 "A" trajectories. If you want to run more trajectories, you can increase the number of runs for each type in the %i2 hash as shown below.

if($type eq "easy")
{
#$i2{"A"}=4; ### old
#$i2{"M"}=10; ### old
$i2{"A"}=6; # run 6 "A" simulations for easy targets
$i2{"M"}=14; # run 14 "M" simulations for easy targets
}
else
{
#$i2{"A"}=6; ###old
#$i2{"M"}=8; ###old
$i2{"A"}=9; # run 9 "A" simulations for hard/medium targets
$i2{"M"}=11; # run 11 "M" simulations for hard/medium targets
}
if($Lch>400)
{ #protein is too big
#$i2{"A"}=0; ### old no ab initio simulations are run for large targets
#$i2{"M"}=15; ### old
$i2{"A"}=0; # no ab initio simulations are run for large targets given the computing required
$i2{"M"}=20; # run 20 "M" simulations for large targets
}
vitamin
Posts: 4
Joined: Fri Apr 30, 2021 3:00 pm

Re: I-TASSER: Change default number (14) of independent runs

Post by vitamin »

Thank you so much for this precise and excellent explanation!
I tried it and it worked :)
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