Cellulose Builder on Max OSX 10.8.3

[roberts...@u.northwestern.edu]

Hello,

I am trying to use the cellulose builder tool to build some crystalline cellulose structures. I am have installed all of the necessary components and properly linked them in my PATH, but am having a strange error occur and am not sure why. When entering the ./cellulose-builder.sh 5 5 5 command in my terminal, I get the following output.

Roberts-MacBook-Pro:cellulose-builder_May_2012 robertsinko$ ./cellulose-builder.sh 5 5 5

 Allomorph I-beta

 Building cristallite with arguments provided ( 5 , 5 , 5 ). 

 PBC = none , no special action regarding translational symmetry will be taken

 (default). Surfaces (1 0 0) and (0 1 0) will be exposed. 

 PCB_c = false , no periodic covalent bonding between  chains' periodic images along direction c (default).

 Building ....

mv: rename crystal.pdb to crystal.pdb.tmp: No such file or directory

 WARNING: Renaming old directory crystal ,

 new name: _crystal_Wed_May__8_14:19:32_CDT_2013

mv: rename crystal.pdb to crystal/crystal.pdb: No such file or directory

mv: rename crystal.psf to crystal/crystal.psf: No such file or directory

 Unexpected error! Oops, this is embarassing...

If you could provide any guidance as to what might be happening, I'd appreciate it.

Thanks!

Rober Sinko, PhD Student

Northwestern University

[roberts...@u.northwestern.edu]

Sorry, the subject should read Mac OSX 10.8.3.

[Thiago Gomes]

Dear Robert Sinko,

we are glad to help. Thanks for reporting.
Please find attached a .tar file which contains a debug version of cellulose-builder based on the errors you reported.

The attached version will not deliver a crystal.pdb file, but should enable us to understand what is causing the error.

Please use this version to run the program as you did earlier (./cellulose-builder 5 5 5 ), leaving the input.inp file as it is, then tar the directory with all its contents and send us back the .tar file you produced. We can thus perform some debugging and help you get cellulose-builder running correctly on your system.

Best Regards,

Thiago C. F. Gomes

2013/5/8 <roberts...@u.northwestern.edu>

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[roberts...@u.northwestern.edu]

Dear Thiago,

Thanks for the quick reply. I've used the new version to run the program just as I had done earlier and have attached the resulting output in the form of a tar file. Let me know if you need anything else from me and thanks again for your help!

Robert

[Thiago Gomes]

Dear Robert,

I guess I've found the problem. Your path to psfgen contains spaces and the program was unaware of how to deal with that.
I've fixed that problem and the version I am sending you attached should run correctly now. I always try to prevent that sort of bug in my programs but one cannot always foresee all possible errors, and that's why it is so important to us to get reports from users.

Please try running the attached version with the same arguments as before (./cellulose-builder 5 5 5) , leaving the file input.inp unchanged.

I have implemented the fix only for allomorph I-beta. Please let me know if it works. If it does work I will implement the same fix for the remainder allomorphs and release a new version of the program on its website.

Again, thaks for reporting!

Best Regards,

Thiago C. F. Gomes

2013/5/13 <roberts...@u.northwestern.edu>