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How can i introduce hydrogen bond as constraint?

Submitted by sp1020 on Mon, 2012-04-02 05:12

Hi everyone,

i need you help~

i am trying to introduce hydrogen bond constraints.

something like this:

Let O on residue 1 and N on residue 10 form hydrogen bond.
Let N on residue 1 and O on residue 20 form hydrogen bond.
etc.

i had tried to place the two hydrogen bond atoms close as distance constraint.

but mostly the distance constraint is not enough

so i want to calculate hydrogen bond as a constraint.

i had tried to use hbonds.HBondSet().

but i can only display hydrogen bond state uwing hbonds.HBondSet().show()

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PyRosetta - General

General Protein Folding Question

Submitted by twopint23oz on Sun, 2012-04-01 22:57

Hello. I have a few questions about abinitio structure prediction.

1) Can abinitio predict secondary structure as well, or does it just take secondary structure as a given based on inputs for fragment picker?

2) Is it worth using Rosetta to fold an 800 AA long protein? Are there some tips/tricks needed to run predictions for such a large protein?

Thanks.

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Rosetta 3 - General

PyRosetta Folding.py script

Submitted by twopint23oz on Sat, 2012-03-31 12:28

I am trying to run the folding.py sample script using the test_in.pdb, frag3 and frag9 files, but I am getting this error:

AttributeError Traceback (most recent call last)

/usr/local/src/pyrosetta/input/folding.py in ()
508 kT , long_inserts , short_inserts , cycles ,
509 jobs , job_output ,
--> 510 PyMOL_Mover_ip , disulfides )
511
512 ################################################################################

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PyRosetta - Scripts

Rosetta 3.4 installation on fedora core 14

Submitted by bharat_46010 on Thu, 2012-03-29 16:50

Hi,

I am trying to install Rosetta3.4 on fedora 14 platform. I am getting the following error after issuing the command : scons bin mode=release

ObjexxFCL -lz -lcppdb -lsqlite3
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
scons: *** [build/src/release/linux/2.6/64/x86/gcc/4.5/libutility.so] Error 1
scons: building terminated because of errors.

Pls guide ??

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Rosetta 3 - Build/Install

how to use AbinitioRelax.mpi.linuxgccrelease?

Submitted by albumns on Mon, 2012-03-26 22:50

hello:
I've compiled Rosetta with MPI option and I am trying to use AbinitioRelax.default.linuxgccrelease by command:

mpiexc -n 8 AbinitioRelax.mpi.linuxgccrelease @flags>log &

and I found that there are eight score for each model(eg: model001 model001 ... model001, model002, model002...model002). It seems that Rosetta use eight CPU to generate eight pdb file with the same name and each one overwrite the previous one and we only get the last one in the end.....

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Rosetta 3 - General

Membrane folding - blastpgp error.

Submitted by arthuc01 on Sun, 2012-03-25 14:47

I know that there have been a number of posts about this problems but none of them post solution to this so hopefully someone can help.

I am attempting to run_lips.pl with the following command

/home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl eliza.FASTA eliza.span /home/eliza/ncbi/blastpgp /home/eliza/ncbi/nr /home/eliza/rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl

But I get the error....

Error in alignblast.pl: blast output file eliza.FASTA truncated:
readline() on closed filehandle MSA at /home/eliza/rosetta/rosetta_

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Rosetta 3 - General

Error getting MinMover attributes

Submitted by assaff on Sun, 2012-03-25 10:54

Hi,

I’m experiencing some very strange behavior on part of PyRosetta.

I'm running pre-built PyRosetta v2.011 for ScientificLinux (64 bit, r47657) on Linux 3.0.3 ( x86_64) with Python 2.6.6. I’ll use MinMover as an example, but this happens with many other object types.

I can instantiate, configure and run a MinMover without a hitch, e.g. min_mover.tolerance(0.025) works fine. But when I try to access that information using a getter, i.e. min_mover.tolerance(), I get an ArgumentError.

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PyRosetta - General

Problems with the convergence of docking by the graph

Submitted by Kanorgon on Sun, 2012-03-25 04:56

I have been doing the docking with the program Rosetta
for an antigen-antibody complex
repeated runs and not get a graph
funnel-shaped
because the lowest energy structure
have a higher rmsd 5Ǻ
wanted to know if that's possible
really appreciate the attention you can give me.

PS
attached a file with the results in pdf format

In these cases it will be worth re-do the docking from some of the results, ie, do a re-docking of the structure obtained in order to obtain a better convergence?

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Rosetta++ - Applications

Memory Issues PyRosetta?

Submitted by ast on Sat, 2012-03-24 03:21

Hi,
I´m running a Pyrosetta script on a 300aa protein with 30 mutable residues a packmover and a fastrelax (3 iterations each) on EX-level 4. When I allocate Memory below 16G I often have uncommented script abortions or "bad alloc" failures. Above 16G that never occurs. Now 16G is a lot and a lot more I seemed to need with Rosetta, albeit, not with the exact same job config. Is there a rule of thump concerning memory usage in PyRosetta? Comparisons with rosetta? Does anybody else encountered memory problems?
Thanks!

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PyRosetta - General

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