Plexpepdock with Zn
Submitted by phanvy on Wed, 2014-06-25 06:10
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Docking
meaning of the clustering the output files
Submitted by phanvy on Tue, 2014-06-24 07:11
Category:
Docking
Hello everyone,
Can you help me understand about clustering the decoys after running Plexpepdock? Can you?
Thank you so much
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Plexpepdock with Zn
Submitted by phanvy on Sun, 2014-06-22 22:40
Category:
Docking
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
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Fastrelax problem
Submitted by Pernille on Fri, 2014-06-20 00:16
Category:
Docking
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:
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PUBLICATION using Rosetta as a method
Submitted by phanvy on Thu, 2014-06-19 08:33
Category:
Structure prediction
Docking
Design
Scoring
Enzyme Design
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
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Cluster decoys after running PlexPepDock
Submitted by phanvy on Thu, 2014-06-19 06:03
Category:
Docking
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
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Error when running prepack of PLEXPEPDOCKING
Submitted by phanvy on Wed, 2014-06-18 07:11
Category:
Docking
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
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Paper about Plexpepdock
Submitted by phanvy on Wed, 2014-06-18 06:29
Category:
Docking
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 !!!
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Fastrelax problem
Submitted by Pernille on Tue, 2014-06-17 08:59
Category:
Docking
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:
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How can move peptide on cleft of enzyme on Flexpepdock?
Submitted by phanvy on Thu, 2014-06-05 02:22
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