The Zhang Lab Message Boards

Hi,

At the end of the modeling process there are no model files. There were some copy statement for which it is said that the files (closc and combo) do not exist or cannot be found. This is probably what causes the problem. Any idea how i can resolve this? Thanks!

Bastiaan

Dear Sir/Mam

I had used I-TASSER server for modeling the structure of the protein but I am getting problem with that structure when I am trying to validate it with validation software and the message displayed by it is that information of some of the residues are missing. My Job id is: S74888.
Can I again try to build model with the same sequence.

Sir/Mam, I want to carry this structure for further analysis. I would be very thankful to you if you could please help me out with this problem at the earliest.

Thanks
Gitanjali Tandon

Which templates were used to get slightly different tertiary structures of alpha-1 glycine receptors? (job id S74906)

Hi
I'm using BSP-SLIM to dock small ligands into models predicted by I-Tasser. When I use tyrosine as ligand, the reuslts do not show the ligand. Any Idea why?

Dear I-TASSER Discussion Board,

Error is
5.1 do clustering
No. of trajectory files: 0

I am not sure about the reason behind this error, this might be due to "run simulation job 14 / 14 sh: /usr/bin/bzip2: No such file or directory".
As I am running this on Ubuntu/Debian and bzip2 is at /bin/bzip2. I have changed the line 907 in "copy and unzip trajectories" section of runI-ITASSER.pl from
`/usr/bin/bunzip2 -f $traj{$i}\.bz2`;
to
`/bin/bunzip2 -f $traj{$i}\.bz2`;
and also to
`/bin/bzip2 -f $traj{$i}\.bz2`;
But the error is still same. Also in my datadir I do not have any "tra" files. If possible, please let me know about what can be the possible reasons.

Files in my datadir:

blast.out GGGd_id2 id2sim_3M id2sim_7M in3M.dd in7M.dd init.SSSc node_id2sim_3A node_id2sim_6M out3A out6M pssm.txt
comb8CA.dat GGGf_id2 id2sim_4A id2sim_8M in4A.dd in8M.dd mtx node_id2sim_3M node_id2sim_7M out3M out7M QQQ_id2

Dear I-TASSER Discussion Board,
Whether "FORTRAN STOP" at step 2.4.2 running pair is an error?

1. make seq.txt and rmsinp
2.1 run Psi-blast
2.2 run psipred
2.3 run solve
2.3 run solve
2.4 run pairmod
2.4.1 removing homology templates based on real and 1
2.4.2 running pair ................
FORTRAN STOP
3.1 do threading
start threading QQQ

Hi,

I am running a version of I-TASSER without changing any option flags that I downloaded and it does not seem to be working properly. It will run, but generates multiple errors, most notable multiple trying to divide by 0 in Fortran. I noticed that there was another similar post, but I couldn't use it to help me out. What are your suggestions as to what might be wrong?

Thanks,
Zack

********************************

opteron.crc.nd.edu{ztracy}59: ./runI-TASSER.pl -libdir ~/i-tasser/ -seqname seq.fasta -datadir ~/i-tasser/bin/psipred/ -usrname ztracy
Your setting is:
-libdir =/afs/crc.nd.edu/user/z/ztracy/i-tasser/
-seqname =seq.fasta
-datadir =/afs/crc.nd.edu/user/z/ztracy/i-tasser/bin/psipred/
-usrname =ztracy
-runstyle =serial
-homoflag =real
-idcut =1
-ntemp =20
-nmodel =5
1. make seq.txt and rmsinp
2.1 run Psi-blast
2.2 run psipred
Cannot open weight file!

Bad psipred pass1 file format!

Hi,
We are studying a protein with 4 domains. We have identified specific and different templates for each of these domains, but we don’t have a given template for the whole protein. I would like to know if it is possible to use these 4 templates with the corresponding alignment to guide the I-tasser modeling.
Thank you very much for your help.
gustavo

Hello ITASSER

Is there a way to impose additional restraints for the stand-alone I-TASSER run?

Thanks

Ravi

when I try I-TASSER I have some error as follow，how to deal with it?
$ ./I-TASSERmod/runI-TASSER.pl -libdir /disk2/cxzou/other_software/I-TASSER -seqname 3SC4.fasta -datadir ./workfolder -usrname cxz
Your setting is:
-libdir =/disk2/cxzou/other_software/I-TASSER
-seqname =3SC4.fasta
-datadir =./workfolder
-usrname =cxz
-runstyle =serial
-homoflag =real
-idcut =1
-ntemp =20
-nmodel =5
1. make seq.txt and rmsinp
error: without ./workfolder/seq.fasta

Hi Everyone,

How is TASSER different from a secondary structure prediction server? The TASSER results include secondary structure prediction, but in a recent example, the prediction that accompanies TASSER results showed a coiled loop (C) for the sequence, but the actual structure showed much more secondary structure with helices and other folding. Can you explain the discrepancy?

Here's the job ID:
S73800

We are interested in the IC3 loop that went from residues # 171-376.

Thanks.

H. Levenson

Is there a specific recommendation to align a model structure generated by the Tasser data base with a another pdb generated elsewhere???

Thanks in advance.

Henry

I'm using currently segmer to model multidomain proteins, and I have some problems to interpret the results I've received. In those results are observed many models produced by threading, but are not .pdb, and I don´t know how to convert this data ina structure, and neither if I must join several models. Could you help me? Thank you very much in advance

If a sequence or loop is sent to TASSER for evaluation with modification of constraints for the modeling of a 212 amino acid sequence, should the DIST modification represent the sequential number of the structure from the gpcr i.e ( DIST 223 CA 436 CA 18.2) it was obtained from or simply, start the sequence with the beginning number for the segment submitted i.e (DIST 1 CA 212 CA 18.3) ???? or does it matter???

Thanks in advance,

Henry Levenson

Sir,
I have received an output for the job S72970 (http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S72970/). All five models score identically. The protein structure is not resolved, and I do not have informations about ligands, so I do not know how to perform an alanine scan.
There is a known domain in the structure, but the peptide align partially to more than one model. A literature search was unsuccessfull, in particular it seems not known the position of the protein in the sperm flagella (it is the sperm autoantigen protein 17). nor other useful indications.
What is the best procedure we could suggest to operate the best choice, in this case?
I am grateful to you, for the results and for your attention.
Best regards.
Anna Giulia Cattaneo

I have used I-Tasser server from the same computer in the past without any problems.

This time I envountered follewing error mesage:

Internal Server Error

The server encountered an internal error or misconfiguration and was unable to complete your request.

Does anybody know what is the reason for this?

Hi,

I encountered an error running LOMETS for the first time. Apparently a fortran end of file error during the QQQ threading and involving file zal33.f

Any ideas about what the problem could be?

Rob

***

[rf@viz6-uoguelph I-TASSER]$ /work/rf/I-TASSER/I-TASSERmod/runLOMETS.pl -libdir /work/rf/I-TASSER -seqname seq.fasta -datadir /work/rf/I-TASSER -usrname rf -runstyle parallel
Your setting is:
-libdir =/work/rf/I-TASSER
-seqname =seq.fasta
-datadir =/work/rf/I-TASSER
-usrname =rf
-homoflag =real
-idcut =1
-ntemp =20
-ntop =10
starting time: Mon Jun 13 13:24:18 EDT 2011
pwd: /work/rf/I-TASSER
1. make seq.txt
2.1 run Psi-blast
2.2 run psipred
3.1 do threading
start threading QQQ
At line 522 of file zal33.f
Fortran runtime error: End of file
Illegal division by zero at /work/rf/I-TASSER/QQQ_seq.fasta line 577.
hostname: viz6-uoguelph
starting time: Mon Jun 13 13:24:18 EDT 2011
pwd: /tmp/rf/LMseq.fasta
running Psi-blast .....

Dear discussion board,

Which nr directory should I download?

1. nr.gz at ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
2. nr.00.tar.gz at ftp://ftp.ncbi.nih.gov/blast/db/nr.00.tar.gz
3. nr.02.tar.gz at ftp://ftp.ncbi.nih.gov/blast/db/nr.02.tar.gz
4. nr.03.tar.gz at ftp://ftp.ncbi.nih.gov/blast/db/nr.03.tar.gz
5. nr.04.tar.gz at ftp://ftp.ncbi.nih.gov/blast/db/nr.04.tar.gz
6. nr.05.tar.gz at ftp://ftp.ncbi.nih.gov/blast/db/nr.05.tar.gz
7. nr.tar.gz at ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz. I am not
able to use ftp from ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz

Do I also need to Download checksum files nr.xx.tar.gz.md5 files?
If possible please let me know among these nr files which nr files should I decompress in $libdir/nr?
Do I need to use ncbi blast tools to convert these files into any specific format?

Regards
Manish

Dear Dr. Zhang and I-TASSER Administrators:

I am Kyaw Zeyar Myint, a graduate student from the University of Pittsburgh. I would like to ask for help regarding one of the jobs that I ran on I-TASSER server previously.

The server output link is: http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S51080/

Unfortunately the output link is now expired and I made a mistake by not saving all the results (C-Scores and TM-Scores for the models. I only saved the predicted 3D models.) I am currently using the model 2 for my studies and I will greatly appreciate if you could send me the output results for the job. Or is there any way for me to retrieve the data?

Thank you very much for your help.

Sincerely,
Kyaw

Hello I-TASSER Message Board Admin:

I am curious to find out what options (idcut, ntemp etc.) are usually chosen when a user submits a sequence for modeling from
the I-TASSER webserver? I am running a local I-TASSER (V1.1) job with 1466 amino acid using the options (see below) on a fairly new Linux system
(Intel Xeon, X86_64, Dual Quad-core, 2.8GHz). It is running for the past several days (see below for qstat output). It is still running, and it is at the moment doing, "cas_NHPBRM1sim_". A job on I-TASSER server didn't took this much time (job id: S71149). CPU time was not reported, so, I am not sure how much time it took for this run. Any help would be appreciated.

qstat:
244964.nci ravi grande NHPBRM1sim_2M 21171 -- -- -- 900:5 R 262:3 ibr2n011/0

Command used for parallel run:

runI-TASSER.pl -libdir $libdir -seqname NHPBRM1 -datadir ${MYHOME} -usrname ${USER} -runstyle parallel -idcut 0.3 -ntemp 15 -nmodel 3

Thanks

Ravi

I am wondering if there is anyway to specify that two particular cysteines must form a disulfide bond for a given amino acid sequence? I've tried restraining the distance between the cysteines to 2.0 Angstroms but that didn't necessary force a disulfide bond to form. It would also be appreciated if someone could explain to me what the CONTACT option exactly does.

Hi,
I would like to add inter-atom distance restraints to my model. I can see that this can be done on the web server version, but I can't seem to find how to do this in the standalone version. Is there an option to do this?
Thanks.

Hi again,

I sent a BSM job with a protein receptor and a SMALL non peptide ligand (histamine) whose sdf file is below. Got the same error message :

An error found in the submitted ligand strucutre.
Please check if the ligand has correct file format and chemical structure.

SDF file :
HME_marvin_vmd
3D
Structure written by MMmdl.
18 18 0 0 1 0 999 V2000
1.1520 -0.5180 4.3930 N 0 0 0 0 0 0
0.0860 -1.3160 4.2480 C 0 0 3 0 0 0
-0.5620 -1.0130 3.1100 N 0 0 0 0 0 0
0.1170 -0.0090 2.5260 C 0 0 3 0 0 0
1.2000 0.3060 3.3430 C 0 0 3 0 0 0
-0.2210 0.6130 1.2320 C 0 0 0 0 0 0
0.4820 -0.1150 0.0630 C 0 0 0 0 0 0
0.1540 0.5190 -1.2180 N 0 0 0 0 0 0
1.7840 -0.5390 5.1300 H 0 0 0 0 0 0
-0.1890 -2.0500 4.9020 H 0 0 0 0 0 0
1.9070 1.0270 3.1740 H 0 0 0 0 0 0

Hello everybody,

Since there's no BSP forum, I post here hoping someone will get hooked int othe problem.

When sending a docking job of a peptide ligand to a protein receptor, I get an error message. At first I thought it was because my peptide was too long (17 residues). I reduced it to three residues, but still the same error. I also tried some changes in the sdf file, but to no aval. I list the message and include the sdf file.

Greetings,

CM

MESSAGE:
Job Status
Job was finished with error.
An error found in the submitted ligand strucutre.
Please check if the ligand has correct file format and chemical structure.

SDF file:

peptide name
3D
Structure written by MMmdl.
102102 0 0 1 0 999 V2000
48.5027 5.9988 27.4363 C 0 0 0 0 0 0
48.6438 7.5033 27.6665 C 0 0 0 0 0 0
47.6758 8.2403 27.4918 O 0 0 0 0 0 0
47.4613 5.7682 27.1183 H 0 0 0 0 0 0

hello everybody,

i see there's no bsp-slim board, so i post here.

my question is of a general nature. most docking algorithms dock ligands, be it either small molecules or peptides or proteins to the SURFACES of the receptors (usually proteins). But in many cases, the binding cavity is in the INTERIOR of the receptor and docking algorithms have no clue as to how to get in there. except AutoDock, in which a box can be defined at a presumed internal site in order to orient the ligand for docking, I know of no other algorithm that can do that. BSP seems to be docking also at the surface of the receptor. is there not a way to adress this issue in bsp ? can bsp dock peptides to proteins ? what's the maximum length allowed for the peptides ?

Greetings,

C Maroun

Hello Sir/Madam:

I have a small problem with some of my PBS jobs getting killed (see below for the contents of some of *.err fiels)
because of cput exceeding the limit. The protein that I am modeling has 320 residues. I am running jobs on a local cluster
( Dual processor Quad-core system, Intel Xeon based system; x5560, x86_64, 2.8GHz, ~74GB memory)

Looking at the perl script, runI-TASSER.pl, I think the cput for the template PBS scripts are being set
as follows:

$walltime="walltime=$hour:59:00";

Is it okay to change the variable 'hour', or is there a different way of doing it?

I also ran a job for the same system mentioned above on your online server. It ran successfully with no problems.
Do you set the cput parameter for your PBS batch jobs different than that followed in the "runI-Tasser.pl"?
Any help would be greatly appreciated.

Thanks for your time.

Ravi

----------------------------------
[ravi@abcc2 hsfrp1]$ cat err_HSFRP1sim_4A

Can I-TASSER be run using MPI or PVM parallelization? What's the basis of the current parallelization option?

I am having problem downloading sequence database - stopped each time due to source error. Please advice.

1, I-TASSER server job submission and deletion -> http://zhanglab.ccmb.med.umich.edu/I-TASSER/registration.html

2, I-TASSER message board -> http://zhanglab.ccmb.med.umich.edu/bbs/

3, I-TASSER package download -> http://zhanglab.ccmb.med.umich.edu/I-TASSER/download/

Since these were set for different purposes, they are independent from each other. Please do not waste your time in trying username/password across different accounts. Thanks!

I-TASSER team

Hello Dr. Zhang:

Thanks for letting me download your I-TASSER Suite. Local installation of I-TASSER works fine with your
version of nr database (nt.tar.gz),but, I am not sure how to upgrade the database(see below for the
contents of the latest NCBI nr database). It looks like your "runI-TASSER.pl" ($db="$libdir/nr/nr";)
refers to "nr" file under "nr" directory. Can you tell me how to prepare this "nr" file?
Is it prepared using any of the programs under blast/bin directory?
Thanks very much for your time.
Ravi
contents of nr.tar.gz:
----------------------
nr nr.00.pin nr.00.pni nr.00.psi nr.01.phr nr.01.pnd nr.01.psd nr.01.psq
nr.00.phr nr.00.pnd nr.00.psd nr.00.psq nr.01.pin nr.01.pni nr.01.psi nr.pal
contents of the latest nr database:
----------------------------------
nr.00.phd nr.00.ppd nr.01.phr nr.01.psd nr.02.pnd nr.02.psq nr.03.pog nr.04.phi nr.04.ppi nr.05.pin nr.05.psi