Difference between revisions of "Molecular Dynamics Simulations (PKU)"
From Bioinformatikpedia
(→Short task description) |
(→Selected Models) |
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* Mutation ALA322GLY --> run finished, quality check pending |
* Mutation ALA322GLY --> run finished, quality check pending |
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* Mutation ARG408TRP --> run finished, quality check pending |
* Mutation ARG408TRP --> run finished, quality check pending |
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| + | ==intermediate Structures== |
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| + | |||
| + | * mut408.pdb: input structure with clashing water removed. |
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| + | * mut408_br.pdb: just the protein, no DNA, crystal water, etc.. |
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| + | * mut408_br_0.pdb: 1 file for every chain, if several are present |
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| + | * mut408.pdb2: structure with hydrogens removed |
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| + | * mut408_repair.pdb: correctly numbered |
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| + | * mut408_repair_0.pdb |
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| + | * mut408_dna.pdb: extracted DNA, empty in our case |
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| + | * mut408_water.pdb: contains structural water <15A from the protein |
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| + | * mut408_sc.pdb: sidechains completed/adjusted with scwrl |
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| + | * mut408_nh.pdb: removed hydrogens, added structural water (and DNA) |
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| + | * mut408_solv_tmp.pdb: added ions |
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| + | * mut408_solv.pdb: duplicate water removed |
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| + | * mut408_solv.pdb2: just protein and added DNA (removes water) |
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| + | * mut408_solv_0.pdb: used to create restriction files for every chain (only 1 here) |
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| + | * mut408_solv_min.pdb: structure with minimized solvent (protein fixed) |
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| + | * mut408_solv_min.pdb2: just protein of previous structure, input to create individual files for each chain (see next step) |
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| + | * mut408_solv_min_0.pdb: used to create restriction files for every chain (only 1 here) |
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| + | * mut408_solv_min2.pdb: minimization with only backbone restrained |
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| + | * mut408_solv_min3.pdb: final minimization before MD runs |
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Revision as of 14:01, 27 June 2012
Short task description
This week, we will start the molecular dynamics simulation of our protein with the wildtype and two mutations. The simulation will be analyzed at a later time, see the complete task description for details. A journal will probably not be neccessary...
Selected Models
- Wildtype 1J8U --> jop pending
- Mutation ALA322GLY --> run finished, quality check pending
- Mutation ARG408TRP --> run finished, quality check pending
intermediate Structures
- mut408.pdb: input structure with clashing water removed.
- mut408_br.pdb: just the protein, no DNA, crystal water, etc..
- mut408_br_0.pdb: 1 file for every chain, if several are present
- mut408.pdb2: structure with hydrogens removed
- mut408_repair.pdb: correctly numbered
- mut408_repair_0.pdb
- mut408_dna.pdb: extracted DNA, empty in our case
- mut408_water.pdb: contains structural water <15A from the protein
- mut408_sc.pdb: sidechains completed/adjusted with scwrl
- mut408_nh.pdb: removed hydrogens, added structural water (and DNA)
- mut408_solv_tmp.pdb: added ions
- mut408_solv.pdb: duplicate water removed
- mut408_solv.pdb2: just protein and added DNA (removes water)
- mut408_solv_0.pdb: used to create restriction files for every chain (only 1 here)
- mut408_solv_min.pdb: structure with minimized solvent (protein fixed)
- mut408_solv_min.pdb2: just protein of previous structure, input to create individual files for each chain (see next step)
- mut408_solv_min_0.pdb: used to create restriction files for every chain (only 1 here)
- mut408_solv_min2.pdb: minimization with only backbone restrained
- mut408_solv_min3.pdb: final minimization before MD runs
