RosettaMP: issue with generating .lips4 file

[Anonymous]

Hi Rosetta users,

I am experiencing trouble using RosettaMP to predict membrane protein structures. I am currently following the RosettaMP tutorial, which can be found here (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/membrane-abinitio).

To briefly describe what I have done:

1. generate structure fragments using Robetta server

2. generate a span file using OCTOPUS server and the script, octopus2span.pl

3. generate lipophilicity prediction file (.lips4 file) using run_lips.pl

I confirmed that I have nr database, blastpgp, and alignblast.pl script and when I run the script, run_lips.pl, it actually outputs _.blast file, _.blast.msa, and etc which seem proper. It seems there is no problem in running blastpgp. However, some warnings are followed after the blastpgp step such as 

Use of uninitialized value highest_lipo_index in array element at /Users/siyoungkim/software/rosetta_src_2018.44.60488_bundle/main/source/src/apps/public/membrane_abinitio/run_lips.pl line 201.

Use of uninitialized value within resnum in array dereference at /Users/siyoungkim/software/rosetta_src_2018.44.60488_bundle/main/source/src/apps/public/membrane_abinitio/run_lips.pl line 201.

Use of uninitialized value lowest_lipo_index in array element at /Users/siyoungkim/software/rosetta_src_2018.44.60488_bundle/main/source/src/apps/public/membrane_abinitio/run_lips.pl line 202

I didn’t copy the whole warnings as they look similar with the above warnings. In the .lips4 file, there is only one line printed, “Lipid exposed data: resnum mean-lipo lipophil entropy”, but nothing else. 

My OS is MacOSX and the version of perl is v5.18.2. Thanks for your help in advance.

Best,

Siyoung

[Anonymous]

Hi，ksy141，Have you solved the problem yet, I faced the same problem.

[Anonymous]

Hi,

I have also had problems with this process. Could I ask which version of the nr database you are using, and where you obtained the blastpgp application?

If it is of any help, I have found that the new ab initio TrRosetta deep-learning algorithm on the Robetta server (https://robetta.bakerlab.org) can be quite good at predicting membrane protein structures.  

[Anonymous]

Hi,

I have also had problems with this process. Could I ask which version of the nr database you are using, and where you obtained the blastpgp application?

If it is of any help, I have found that the new ab initio TrRosetta deep-learning algorithm on the Robetta server (https://robetta.bakerlab.org) can be quite good at predicting membrane protein structures.  

[Anonymous]

Has any solution to this been found? I’m having the same issue.

[Anonymous]

Hi all, 

After a few hours in the perl debugger I managed to get this worked out. The issue seems to be that the server called to generate some of the files is dead. The script needed as a text file can be found here: http://tanto.bioe.uic.edu/lips/lips.txt

If you download that, save it as a .pl file and make it an executable, and then make sure the path to call perl in the first line are edited/correct. I also had to remove the -w/-d flag because calling these modes from inside another perl script was causing issues (that might be specific to my set-up). 

Then change the portion of line #127 in run_lips.pl “curl -s $url” to “~WHEREVER-YOU-SAVED-THE-FILE/lips.pl”. 

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