Gaucher Task07 Protocol
From Bioinformatikpedia
Contents
SCWRL
scwrl -i 2nt0_A.pdb -s 2nt0_A_1.seq -o 2nt0_A_1.pdb > 2nt0_A_1.out
FoldX
list.txt
2nt0_A.pdb
mutant_list.txt:
ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKG FGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPL IHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPA KATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL ETISPGYSIHTYLWHRQ ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANRTGTGLLLTLQPEQKFQKVKG FGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPL IHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPA KATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL ETISPGYSIHTYLWHRQ ...
run.txt
2nt0_A.pdb <TITLE>FOLDX_runscript; <JOBSTART>#; <PDBS>#; <BATCH>list.txt; <COMMANDS>FOLDX_commandfile; <BuildModel>#,mutant_file.txt; <END>#; <OPTIONS>FOLDX_optionfile; <Temperature>298; <R>#; <pH>4.5; <IonStrength>0.050; <water>-CRYSTAL; <metal>-CRYSTAL; <VdWDesign>2; <OutPDB>true; <pdb_hydrogens>false; <complex_with_DNA> true; <END>#; <JOBEND>#; <ENDFILE>#;
foldx -runfile run.txt
Minimise
Remove hydrogens and waters:
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1.pdb -noh -jprot >2nt0_A_1_re.pdb
Minimise:
/opt/SS12-Practical/minimise/minimise 2nt0_A_1_re.pdb 2nt0_A_1_1.pdb > 2nt0_A_1_1.out /opt/SS12-Practical/minimise/minimise 2nt0_A_1_1.pdb 2nt0_A_1_2.pdb > 2nt0_A_1_2.out /opt/SS12-Practical/minimise/minimise 2nt0_A_1_2.pdb 2nt0_A_1_3.pdb > 2nt0_A_1_3.out /opt/SS12-Practical/minimise/minimise 2nt0_A_1_3.pdb 2nt0_A_1_4.pdb > 2nt0_A_1_4.out /opt/SS12-Practical/minimise/minimise 2nt0_A_1_4.pdb 2nt0_A_1_5.pdb > 2nt0_A_1_5.out
Gromacs
repairPDB:
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1.pdb -noh -jprot > 2nt0_A_1_re.pdb
SCWRL:
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2nt0_A_1_re.pdb -o 2nt0_A_1_re_sc.pdb
repairPDB again:
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1_re_sc.pdb -noh -jprot > 2nt0_A_1_ready.pdb
pdb2gmx, then select: 1=AMBER03 protein, nucleic AMBER94, 8=CHARMM27 all-atom force field (with CMAP), 14=OPLS-AA/L all-atom force field :
/opt/SS12-Practical/gromacs/bin/pdb2gmx -f 2nt0_A_1_ready.pdb -o 2nt0_A_1.gro -p 2nt0_A_1.top -water tip3p
or /opt/SS12-Practical/gromacs/bin/pdb2gmx -f 2nt0_A_1_ready.pdb -o 2nt0_A_1.gro -p 2nt0_A_1.top -water tip3p -ff amber03
Create a MDP file 'file.mdp' with the following content:
title = PBSA minimization in vacuum cpp = /usr/bin/cpp # Preprocessing # -DFLEXIBLE: include flexible water in stead of rigid water into topology # -DPOSRES: includes posre.itp into topology, used for position restraints. define = -DFLEXIBLE -DPOSRES # Implicit solvent - simulation with implicit solvent using the Generalized Born formalism implicit_solvent = GBSA # Run control - steepest descent algorithm for energy minimization integrator = steep # Run control - tolerance emtol = 1.0 # Run control - maximum number of steps to integrate or minimize nsteps = 500 # Output - frequency to write energies to energy file nstenergy = 1 # Tables - group(s) to write to energy file energygrps = System # Neighbour searching - makes grid in the box and only check atoms in neighboring grid cells when constructing a new neighbor list every nstlist steps ns_type = grid # Electrostatics - twin range cut-off's with neighborlist cut-off rlist and Coulomb cut-off rcoulomb coulombtype = cut-off rcoulomb = 1.0 # VDW - distance for the LJ or Buckingham cut-off rvdw = 1.0 # Bonds - no constraints except for those defined explicitly in the topology constraints = none # Neighbour searching - Use no periodic boundary conditions, ignore the box. pbc = no
grompp:
/opt/SS12-Practical/gromacs/bin/grompp -v -f file.mdp -c 2nt0_A_1.gro -p 2nt0_A_1.top -o 2nt0_A_1.tpr
Minimise system:
/opt/SS12-Practical/gromacs/bin/mdrun -v -deffnm 2nt0_A_1
Analyze the minimization, and select 1=Bond, 2=Angle and 12=Potential:
/opt/SS12-Practical/gromacs/bin/g_energy -f 2nt0_A_1.edr -o 2nt0_A_1.xvg