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example scripts for comparative modeling

Submitted by fglaser on Sun, 2011-02-27 21:50

Hi All,

I am completely new to Rosetta, so forgive me for the trivial questions. I would like to run comparative modeling with rosetta, does anybody has a good simple tutorial or script examples?

I am aware about the online manual info, but it is not detailed enough...

Every information will be highly appreciated!

Have a good day,

Fabian Glaser
Technion, Israel

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Rosetta 3 - Applications

ERROR READING PDB FILE

Submitted by asmi on Sat, 2011-02-26 07:23

I am new to rosetta3.0. As i am trying to perform denovo modelling of RNA molecule my script is giving an error again and again like this:

ERROR: unrecognized aa r
ERROR:: Exit from: src/core/io/pdb/file_data.cc line: 476

I have already changed the PDB file format so that res name reads rA, rG, rU, and rC. But still i am getting this message.Can someone suggest whats going wrong?

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Rosetta 3 - General

refinement or idealization of a dimeric protein

Submitted by anusmita on Wed, 2011-02-23 22:23

Hii All

I am looking forward for idealizing and then refining a dimeric protein , but, using a fragment library for a monomeric protein. Use of a dimeric fragment library joins the two monomers into one single protein chain.

Thanking you

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Rosetta++ - Applications

Error while executing rosetta 3.1 loop modeling

Submitted by bharat_46010 on Wed, 2011-02-23 18:52

Hi,

I build the rosetta 3.1 on fedora core 6 and after that I used the loop modeling demo ... while issuing the loop modeling command . I got the following error :-
[root@bmel LoopModeling]# ./loopmodel.linuxgccrelease
./loopmodel.linuxgccrelease: error while loading shared libraries: libprotocols.so: cannot open shared object file: No such file or directory

Also its happening for all the .exe files in bin folder ....

Can anybody tell me how can I rectify this error ??

Thanks in advance for help ..

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Rosetta 3 - Build/Install

Patches for post-translational modifications

Submitted by ltrabuco on Tue, 2011-02-22 01:00

Dear all,

I see that patches exist supporting several post-translational modifications, but I don't know how to enforce that a patch be applied to my structure. I have, for instance, a phosphorylated Ser residue (SEP), which is not recognized by Rosetta. I assume I need to rename it to SER and apply the patch found in rosetta-3.2/rosetta_database/chemical/residue_type_sets/fa_standard/patches/ser_phosphorylated.txt, but I couldn't find how to assign patches in the current documentation.

Thanks in advance!

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Rosetta 3 - General

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