Gaucher Disease: Task 09 - Lab Journal: run minimise.sh

From Bioinformatikpedia
Revision as of 19:10, 1 September 2013 by Kalemanovm (talk | contribs) (Created page with "==run_minimise.sh== <source lang='bash'> #!/bin/sh ##first run repairPDB to remove hydrogens, waters and hetero atoms: #/opt/SS12-Practical/scripts/repairPDB <input.pdb> -noh -…")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

run_minimise.sh

<source lang='bash'>

  1. !/bin/sh
    1. first run repairPDB to remove hydrogens, waters and hetero atoms:
  1. /opt/SS12-Practical/scripts/repairPDB <input.pdb> -noh -jprot > <output.pdb>
  1. WT

cd ~/master_practical/Assignment9_Structure-based_mutation_analysis/ /opt/SS12-Practical/scripts/repairPDB scwrl/2V3E_B_WT_backbone_IN.pdb -noh -jprot > minimise/input_noh_nohoh/2V3E_B_WT.pdb

  1. SCWRL

for mutation in "S38R" "N102S" "G202E" "N370S" "L444P"; do /opt/SS12-Practical/scripts/repairPDB scwrl/2V3E_B_${mutation}_model_OUT.pdb -noh -jprot > minimise/input_noh_nohoh/scwrl/2V3E_B_${mutation}_scwrl.pdb; done

  1. foldX

for i in 1 2 3 4 5; do /opt/SS12-Practical/scripts/repairPDB foldX/output_files/2V3E_B_${i}.pdb -noh -jprot > minimise/input_noh_nohoh/foldx/2V3E_B_${mutation}_foldx.pdb; done

    1. then minimise:
  1. /opt/SS12-Practical/minimise/minimise <input.pdb> <output.pdb> > <log file>
  1. WT

cd ~/master_practical/Assignment9_Structure-based_mutation_analysis/minimise/output/ minimise="/opt/SS12-Practical/minimise/minimise"

base="2V3E_B_WT" $minimise ../input_noh_nohoh/${base}.pdb wt_minimised/${base}_minimised_round1.pdb > wt_minimised/${base}_minimised_round1_log.txt

  1. 4 more rounds:

for n in 2 3 4 5; do let p=$n-1; $minimise wt_minimised/${base}_minimised_round${p}.pdb wt_minimised/${base}_minimised_round${n}.pdb > wt_minimised/${base}_minimised_round${n}_log.txt; done

  1. foldX

for mutation in "S38R" "N102S" "G202E" "N370S" "L444P"; do base="2V3E_B_${mutation}_foldx" $minimise ../input_noh_nohoh/foldx/${base}.pdb foldx_minimised/${base}_minimised_round1.pdb > foldx_minimised/${base}_minimised_round1_log.txt

  1. #4 more rounds:

for n in 2 3 4 5; do let p=$n-1; $minimise foldx_minimised/${base}_minimised_round${p}.pdb foldx_minimised/${base}_minimised_round${n}.pdb > foldx_minimised/${base}_minimised_round${n}_log.txt; done done

  1. SCWRL
  2. ->did not work with SCWRL models after removing Hs and HETATMs repairPDB! different errors,two last:
  3. Unable to find atom 1H in ALA
  4. Could not get GATOM for (ALA11H )
  5. ran openbabel locally like this:

cd ~/Documents/Studium/Master/SS13/MasterPractical/Assignment9_Structure-based_mutation_analysis/minimise/input_noh_nohoh/scwrl/ for mutation in "S38R" "N102S" "G202E" "N370S" "L444P"; do sudo /home/maria/Documents/Studium/Master/SS13/MasterPractical/Assignment9_Structure-based_mutation_analysis/openbabel/build/bin/obabel -ipdb 2V3E_B_${mutation}_scwrl.pdb -opdb 2V3E_B_${mutation}_swrl_obabel-d.pdb -d > 2V3E_B_${mutation}_scwrl_obabel-d.pdb done

  1. -> sudo and piping in the same pdb file as given after -opdb, because it only wrote in the file like this.
  2. -> First mutation created 2 models, separated manually in one model per file like this:
  1. sed -n '2,7874p' 2V3E_B_S38R_scwrl_obabel-d.pdb > 2V3E_B_S38R_scwrl_obabel-d_model1.pdb
  2. [sed -n '7877,15749p' 2V3E_B_S38R_scwrl_obabel-d.pdb > 2V3E_B_S38R_scwrl_obabel-d_model2.pdb]
    1. [checked that repairPDB -jprot (withoutl -noh), then obabel -d makes no difference.
  1. ran minimise with the first model of S38R:

base="2V3E_B_S38R_scwrl_obabel-d_model1" $minimise ../input_noh_nohoh/scwrl/${base}.pdb scwrl_minimised/${base}_minimised_round1.pdb > scwrl_minimised/${base}_minimised_round1_log.txt

  1. 4 more rounds:

for n in 2 3 4 5; do let p=$n-1; $minimise scwrl_minimised/${base}_minimised_round${p}.pdb scwrl_minimised/${base}_minimised_round${n}.pdb > scwrl_minimised/${base}_minimised_round${n}_log.txt; done

  1. ran minimise with the models of the remaining four mutations:

for mutation in "N102S" "G202E" "N370S" "L444P"; do base="2V3E_B_${mutation}_scwrl_obabel-d" $minimise ../input_noh_nohoh/scwrl/${base}.pdb scwrl_minimised/${base}_minimised_round1.pdb > scwrl_minimised/${base}_minimised_round1_log.txt #4 more rounds: for n in 2 3 4 5; do let p=$n-1; $minimise scwrl_minimised/${base}_minimised_round${p}.pdb scwrl_minimised/${base}_minimised_round${n}.pdb > scwrl_minimised/${base}_minimised_round${n}_log.txt; done done </source>