The problem hasn't been solved
Hi,
I'm trying to get PyRosetta installed on my windows 10 laptop. I've followed all of the instructions listed here: http://www.pyrosetta.org/documentation/windows
Dear Friends,
I am running ab initio rosetta run using openmpi:
mpiexec -np 16 /main/source/bin/AbinitioRelax.mpi.linuxgccrelease -database /main/database/ @options -mpi_tracer_to_file log > log1.log &
I see "score.fsc" file in the folder with 2000 models, and generated a RMSD vs Energy plot, whcih gives me this (the attached plot)
Hi all,
Just trying to model a small molecule and how it interacts w/ my bigger protein in pyrosetta.
I got this far:
pose2 = Pose()
nonstandard_residue_set = generate_nonstandard_residue_set(pose2, ["ARA2.params"])
pose = pose_from_pdb(nonstandard_residue_set, "combine.pdb")
But pose_from_pdb only takes only 1 argument, how do I get around this?
Dear Friends,
I am performing de novo structure prediction for a 1135 amino acid long sequence. I ran robetta server to generate fragments for my 1135 amino acid long sequence, but got the error : Sequence length must be between 27 and 1000 residues
Can you please et me know how to get fragments in this scenario? Thanks!
Dear Friends,
I have successfully built "mpi" binaries on my ubuntu 18.04. I want to run rosetta on my centos6.9 (with "Openmpi") machine too; can I simply copy the binaries from my ubuntu to centos and run rosetta using "mpi" there? thank you!
Dear Friends,
I downloaded rosetta static binaries "Rosetta 3.10 source + binaries for Linux - as one bundle (13G)" on my centos6.9. I can see that the executable in the "main/source/bin" are working, but how can I run these static executables (such as "AbinitioRelax.static.linuxgccrelease" ) on multple CPUs? Can I use "mpiexec" with these executables?
Thanks!
Dear Friends,
I am trying to install rosetta on centos 6.9 as a non-root user. Python version is 2.7. OPenmpi is installed too. But, when I run this below command I get this error: (it's the end section of the error)
Dear friends,
As a new learner of rosetta, I encountered an error "chain_id A represents more than one chain!" after I downloaded the 5ugy.pdb file from RCSB PDB database and renumbered to the AHo Scheme with PyIgClassify Server.
If anyone can help me with this issue? Any help would be appreciated.
Hi all:
I am going to use antibody.default.linuxgccrelease to make a model for an antibody sequence. The command I entered is ”antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database /home/mxp/apps/rosetta/tools/antibody >error1.log“. I encountered the following error:
.......
core.conformation.Conformation: current variant for 207 CYD
core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner
caught exception
Dear Friends,
When running formatdb like this:
blast/bin/formatdb -o T -i nr_pfilt
[formatdb] ERROR: Using 1000000000 bases per volume will exceed the maximum number
of volumes formatdb can create.
Please increase this value or do not set it at all.
I get the above error, can you please let me know how can I resolve this issue?
Thanks!