The problem hasn't been solved
Hello! I want to get the RMSD between the original ligand nd the one i designed. both the ligands are peptides of different lenght (the one i designed is smaller).
I tried to use calc_Lrmsd(pose1,pose2) but i got the following error:
Hello everyone,
I ran Docking with structure which have Zn. Now, I want to run Plexpepdock with structure with Zn. But, program can not recongnize it. I want to run Plexpepdock with Zn. What should I do?
Thank you so much !
Best regards.
Tuong Vy
How can I create a pose from sequence containing acetylated lysine?
Using p = pose_from_sequence("VSK[LYS_p:N_acetylated]GPF","fa_standard") and then dumping it gives a pdb with two chains and the K residue is not modified.
thanks!
Hello everyone,
Can you help me understand about clustering the decoys after running Plexpepdock? Can you?
Thank you so much
I got the energy score using score3 setting. I heard that the unit of this energy score is not kcal/mol, and there is a conversion factor.What's the unit of Rosetta energy function? Where can I find some documents about this?
Hello everyone,
I ran Docking with structure which have Zn. Now, I want to run Plexpepdock with structure with Zn. But, program can not recongnize it. I want to run Plexpepdock with Zn. What should I do?
Thank you so much !
Best regards.
Tuong Vy
I'm using PyRosetta-r21 on Ubuntu togather with IPython 2.0.0 notebooks. This works extremly well, with one small problem:
Some output is redirected to the console in which "ipython notebook" command was started instead of the notebook cell.
So the question is: is it possible to capture the output of scorefxn.show(pose)?
I have tried to use the example in "test/T007_TracerIO.py"
Dear all,
There may be some minor mistakes in the SetPyRosettaEnvironment.sh in the r21 release of PyRosetta:
On line 34 "export LD_LIBRARY_PATH=$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
$PYROSETTA is not added to the LD_LIBRARY_PATH and "libboost_python.so.1.55.0.so" is consequently not found.
Corrected: "export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
(Or just move the offending so to rosseta subdir)
Is it possible to approxmate the CHARMM energy (function) by the rosetta scoring function?
As a starting point I could work with fixed angles and bond lengths, so I guess setting the weghts for fa_atr, fa_rep and fa_elec to 1 and all the rest to zero is a good start. But is it possible to somehow load the CHARMM diheral parameters?
Thank you for your help,
Ajasja Ljubetič
