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error while building rosetta++

Hello

I am new to rosetta. When i am trying to build rosetta by typing make gcc,i am getting a long message a part of which looks like this:

src/utility/io/zipstream.ipp:657: instantiated from ‘void zlib_stream::basic_zip_ostream::add_footer() [with Elem = char, Tr = std::char_traits, ElemA = std::allocator, ByteT = unsigned char, ByteAT = std::allocator]’

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Username and Password for download link?

Hello,

I applied for the express academic license for pyrosetta and received the license email very rapidly. However, as compared to the Rosetta license where I also received an email with the download link and username and password, I did not receive such for Pyrosetta. Any ideas?

Thanks so much,

Judy

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excecutable files don't work -- Rosetta3.2 on WindowsXP

Hi
I tried installing rosetta 3.2 on windows XP using cygwin1.7, gcc 3.4.4. following a procedure posted on 10/20/2009.

It seems I was able to compile rosetta3.2. There are "executable files" in rosetta_source/bin folder and rosetta_source/build/src/release/cygwin/1.7/32/x86/gcc folder. They look like AbinitioRelax.cygwingccrelease, backrub.cygwingccrelease and so on.

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Fragment files for membrane_abinitio application

Hi

I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta

The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.

Could anyone please help in this matter ?

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How to estimate the effect of a mutation on the binding energy?

Given a protein complex, I would like to estimate the effect of a point mutation on the binding energy (ddG). I'd appreciate if anyone could point me to the Rosetta app(s) that I should look into. I'm fairly new to Rosetta.

Thanks!

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how to relax structure constraining CA in Rosetta3.2?

Hi

I am wondering how to relax structure constraining CA in Rosetta3.2?

I found that each protocol contains two executable command such as:

relax.default.linuxgccrelease relax.linuxgccrelease

is there any differences between these two?

THX

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Fragment files for membrane_abinitio application

Hi

I am trying to make fragment files for membrane_abinitio application. I have secondary structure prediction results (*.rdb files) from SAM secondary structure server. I am trying to run the command:
make_fragments.pl -nojufo -nopsipred -noprof -samfile HRG3_all_X.t2k.str2.rdb HRG3.fasta

The program is generating all the files (.cst, .a2m) but somehow its not generating fragment (frag3, frag9) files at all.

Could anyone please help in this matter ?

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is it possible to ab initio only a part of a protein?

I've built a homology model but a part of it (around 12aa)is not reliable because there is no homology template in this region. The whole protein is around 350aa. And I am wondering is it possible built a ab init model based on my initial model to complete these unreliable region?

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How to design a stand-alone loop from a binding interface?

Hi, Dear colleagues!

I am new to Rosetta and am now finding whether there is a solution to my problem using powerful Resetta.

I want to cut a loop which is responsible for the binding of A to B from protein A. I need to constrain this loop so it will maintain its bound conformation though it is now in the apo form.

The problems are:
1) I need to find a way to automatically constrain it either by using disulfide bond and cyclization;
2) The loop is disulfide-bonded to the rest of the protein and this disulfide bond may be responsible for maining a turn in its bound conformation;

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Rosetta Docking server

Dear Sir or Madam,

I got a problem when I was trying to submit my pdb file to Rosetta docking server. I got the message as following,

"Occupancy Error: Submitted PDB(s) have occupancy field other then '1.0'. Currently we only accept PDB's with occupancy field equal '1.0'. Please fix occupancy field and resubmit the job."

Do you know how to change occupancy field of pdb file?

Regards,

Zhanjun Hou
Karmanos Cancer Center
houz@karmanos.org

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