Zhanglab forum

$ sudo perl /mnt/c/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /home/user/ITLIB -seqname seq -datadir /mnt/c/I-TASSER5.1/example -datadir /mnt/c/I-TASSER5.1/example

Your setting for running I-TASSER is:
-pkgdir = /mnt/c/I-TASSER5.1
-libdir = /home/user/ITLIB
-java_home = /usr
-seqname = seq
-datadir = /mnt/c/I-TASSER5.1/example
-outdir = /mnt/c/I-TASSER5.1/example
-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 143 residues:
> seq
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.1 run Psi-blast
2.2 Secondary structure prediction was done before.
2.3 Predict solvent accessibility...
2.4 run pairmod
pair exist
3.1 do threading
/mnt/c/I-TASSER5.1/example/init.PPAS exists
/mnt/c/I-TASSER5.1/example/init.dPPAS exists
/mnt/c/I-TASSER5.1/example/init.dPPAS2 exists
/mnt/c/I-TASSER5.1/example/init.Env-PPAS exists
start serial threading MUSTER
/tmp/root/ITseq
/mnt/c/I-TASSER5.1/example/MUSTER_seq
Illegal division by zero at /mnt/c/I-TASSER5.1/example/MUSTER_seq line 599.
hostname: STATION-PCMC
starting time: Sat May 20 09:34:01 CEST 2023
pwd: /tmp/root/ITseq
running Psi-blast .....
running zalign .....


/mnt/c/I-TASSER5.1/example/init.wPPAS exists
/mnt/c/I-TASSER5.1/example/init.wdPPAS exists
/mnt/c/I-TASSER5.1/example/init.wMUSTER exists
3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0

Dear user,

Can you check if init.dat file exists in /mnt/c/I-TASSER5.1/example folder?

Best
IT Team

Hi
Thank you for your responce

Yes i have inti.dat in the folder /I-TASSER5.1/example

Dear user,

It seems the template file is correctly generated. Could you 'ls' your example folder, or zip the example folder and attach in the response

Best
IT Team

Hello

Yes I can

I have try to do with 2 different computer and with version 5.1 and 5.2 always the same problem

Can you please help me according to attached file

Dear user,

Thank you for your files, we are working on debugging the program and will let you know the issue ASAP.

Best
IT Team

Dear user,

Can you change your parameters "-seqname seq " to "-seqname example " if your folder name is "example", and see if you can go though?

Best
IT Team

hello
I have try this
sudo perl /mnt/c/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /home/user/ITLIB -seqname example -datadir /mnt/c/I-TASSER5.1/example -datadir /mnt/c/I-TASSER5.1/example

the result is :

(base) user@STATION-PCMC:/mnt/c/I-TASSER5.1$ sudo perl /mnt/c/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /home/user/ITLIB -seqname example -datadir /mnt/c/I-TASSER5.1/example -datadir /mnt/c/I-TASSER5.1/example

Your setting for running I-TASSER is:
-pkgdir = /mnt/c/I-TASSER5.1
-libdir = /home/user/ITLIB
-java_home = /usr
-seqname = example
-datadir = /mnt/c/I-TASSER5.1/example
-outdir = /mnt/c/I-TASSER5.1/example
-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 143 residues:
> example
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.1 run Psi-blast
2.2 Secondary structure prediction was done before.
2.3 Predict solvent accessibility...
2.4 run pairmod
pair exist
3.1 do threading
/mnt/c/I-TASSER5.1/example/init.PPAS exists
/mnt/c/I-TASSER5.1/example/init.dPPAS exists
/mnt/c/I-TASSER5.1/example/init.dPPAS2 exists
/mnt/c/I-TASSER5.1/example/init.Env-PPAS exists
start serial threading MUSTER
/tmp/root/ITexample
/mnt/c/I-TASSER5.1/example/MUSTER_example
Illegal division by zero at /mnt/c/I-TASSER5.1/example/MUSTER_example line 599.
hostname: STATION-PCMC
starting time: Tue Jun 6 02:06:26 CEST 2023
pwd: /tmp/root/ITexample
running Psi-blast .....
running zalign .....


/mnt/c/I-TASSER5.1/example/init.wPPAS exists
/mnt/c/I-TASSER5.1/example/init.wdPPAS exists
/mnt/c/I-TASSER5.1/example/init.wMUSTER exists
3.2 make restraints
4.1 run simulation
run 14 serial simulations
run simulation job 1 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 2 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 3 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 4 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 5 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 6 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 7 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 8 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 9 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 10 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 11 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 12 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 13 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
run simulation job 14 / 14
bzip2: Can't open input file rep*.tra: No such file or directory.
5.1 do clustering
No. of trajectory files: 0

Dear user,

We tested your example files and ran with your files as the start point and got the correct results. So the input files of this case for the I-TASSER simulation should be ready. We think you should have some issues with the simulation itself.

I may want to check the following setting is correct on your system,

1. do you have gfortran installed on your system?
2. please go to /mnt/c/I-TASSER5.1/example folder. There should be a script named 'examplesim_1A'. Please directly run this script to see what the output message is.

Best
IT Team