Gaucher Task07 Protocol

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Revision as of 13:27, 25 June 2012 by Zhangg (talk | contribs) (Gromacs)

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