Hello everyone,
Can you help me understand about clustering the decoys after running Plexpepdock? Can you?
Thank you so much
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
Hi all
I am docking several different proteins and before docking I use fastrelax to relax the individual proteins.
Fir some of the proteins (they are all less than 200 aa) Fastrelax takes extreemly long to generate 25 poses.
For one in particular following error pops up:
Hello everyone,
I try to find public paper which use Rosetta as a method, but I can not see. If you have read any paper have used Rosetta protocols , please give me some.
Thank you so much
Hello everone
After running the Plexpepdock, I have 40000 decoys. I try to use the cluter program of Rosetta 3.4 . But, I do not understand the meaning of cluster. Because , after I tried to run with 200 decoys and get the out:file with 200 file c.0.XXX.pdb format. I do not understand how cluster work.
Flags:
-in:file:silent decoys.silent
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-in:file:fullatom
-score:weights
-score:patch
-cluster:sort_groups_by_energy
Hello everyone!
I use Plexpepdocking (Rosetta 3.4), in my structure have one ion Zn , but Plexpepdock can not recognize it.
Please take a look on my pdb file and tell me how to fix this Error.
Thank you so much for your help.
Thank!!!
this is the flag for pre_packing
-s tryzn.pdb
-database /home/tuongvy/SW/rosetta3.4/rosetta_database
-flexpep_prepack
-ex1
-ex2aro
This is the ERROR
ERROR: unknown atom_name: ZN CA
ERROR:: Exit from: src/core/chemical/ResidueType.cc line: 1692
Hello everyone,
I want to have some paper about using Plexpepdock to find binding site of peptite on its receptor (in my case) is protein. Some one can help me? I try to find but I get anything.
Thank you so much !!!
Hi all
I am docking several different proteins and before docking I use fastrelax to relax the individual proteins.
Fir some of the proteins (they are all less than 200 aa) Fastrelax takes extreemly long to generate 25 poses.
For one in particular following error pops up:
I am currently trying to set up a docking run between two proteins that have compatible symmetry, and almost certainly interact along a 3-fold symmetry axis. One molecule is trimeric, the other is a D3 hexamer, with protomeric MWs of 20 and 25 kDa respectively. I have experimental (x-ray) structures for both proteins, and an initial model where the two proteins are in contact, and lined up with the 3-fold axis of each along Z. I therefore want to search only rotations around Z, along with a small Z-translation shift.
