The problem has been solved
I have been running abinitio on a server using mpi to utilize 13 cores. There have been a few times over the last month when we had to restart abinitio. My question is will abinitio pick up the fold count where it left off, or will it start the count from one again?
Hi all,
I am trying to use the Molecular Replacement functions of Rosetta (mr_protocols), and all seems to work well as I go through the example.
However, I am trying to solve the structure of a protein with two chains, and I am getting confused on how to handle this with the alignment files. For instance, I have grabbed the hhr files from the HHpred server, but I can only submit a single chain at a time.
Is there a way to combine the hhr files for each chain, so that I can use it with mr_protocols???
Any advice would be appreciated. I am at a complete loss here.
Many thanks,
Dear everyone,
After applying FlexPepDocking, I got a silent output file. Then, I use cluster command to cluster the result files. Although the program gives the structure of each group, it is still difficult to decide which structure I should choose for further analysis. For me, I want the following statistics of the clustering result:
1.Sorting the binding energy of the structures in each group.
2.Binding Energy of each structure, so I can plot an "Energy-structure index" graph to decide how many structures I should consider for each group.
Is there any scripts or suggestions?
Hello,
How does Rosetta3.x handle degenerate protons or how do I implement those in a constraint file?
I am trying to add NMR derived constraints for methyl-groups to my AbInitio Modelling. I found a reference and the corresponding website that describes this issue in Rosetta2.3 (http://www.rosettacommons.org/guide/NMR).
However, adding either
AmbiguousNMRDistance HG2# 3 H 11 BOUNDED 1.5 5.00 0.3
or
AmbiguousNMRDistance #HG2 3 H 11 BOUNDED 1.5 5.00 0.3 (with -IUPAC flag)
results in errors similar to the following:
std::cerr: Exception was thrown:
Hi,
Everyone, I want to fix the position of the unrecognized SEP(phospho-Serine) in my peptide and use BindingSite Or Constant Or Coordinate constrains in the constrain site. Could anyone here show me an example of how to write such a constrain file?
There are some examples in "http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/co..." but the restrains I need seems much difficult than the examples there.
Thanks and Regards,
Yuan SHANG
Hi,everyone,
I'm new to rosetta peptide docking. Currently, I want to dock a peptide into protein using Flexpep docking. But there is a phosphorylation in my peptide and when I use "-remember_unrecognized_res" flags, after docking the peptide is discontinuous at the phosphorylation site. Anyone knows how to solve this problem?
Thanks in advance.
Yuan
Hello all,
I am trying to make iterations between KIC and fbb. fbb design accepts multiple inputs through -l option. I cant find a similar option for KIC. I can only input one pdb at a time using the option -loops:input_pdb. I tried putting multiple pdbs using -loops:input_pdb but it gave me: ERROR: Multiple values specified for option -loops:input_pdb.
any help will be great.
Thank you
a_s_a
How to use Rosetta to do Position constraint docking？I am eager to know it.
To help the building from source on Debian and Ubuntu, which is not completely straight forward on the now current versions of gcc/g++ on these platforms, I have prepared all that would be required for a basic Debian/Ubuntu package. The Rosetta license does not allow the distribution of the packages through Debian, obviously.
Hello everyone:
When I run "/rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl",I got the error that:
[root@localhost input]# /rosetta/rosetta_source/src/apps/public/membrane_abinitio/run_lips.pl t2.fasta t2.span /rosetta/blast/bin/blastpgp /rosetta/nr /rosetta/rosetta_source/src/apps/public/membrane_abinitio/alignblast.pl
Error in alignblast.pl: blast output file t2.blast truncated: