Difference between revisions of "Gaucher Task07 Protocol"

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(Gromacs)
 
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  +
== Sources ==
  +
You can checkout the git repository containing all relevant data an scripts by:
  +
<pre>
  +
git clone /mnt/home/student/angermue/mp/tasks/task07
  +
</pre>
  +
 
== SCWRL ==
 
== SCWRL ==
 
<pre>
 
<pre>
Line 58: Line 64:
 
foldx -runfile run.txt
 
foldx -runfile run.txt
 
</pre>
 
</pre>
  +
  +
== 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 ==
 
== Gromacs ==
Line 63: Line 83:
 
repairPDB:
 
repairPDB:
   
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1.pdb -jprot > output/2nt0_A_1_re.pdb
+
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1.pdb -noh -jprot > 2nt0_A_1_re.pdb
   
 
SCWRL:
 
SCWRL:
   
/opt/SS12-Practical/scwrl4/Scwrl4 -i output/2nt0_A_1_re.pdb -o output/2nt0_A_1_re_sc.pdb
+
/opt/SS12-Practical/scwrl4/Scwrl4 -i 2nt0_A_1_re.pdb -o 2nt0_A_1_re_sc.pdb
   
  +
repairPDB again:
pdb2gmx:
 
  +
  +
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1_re_sc.pdb -noh -jprot > 2nt0_A_1_ready.pdb
  +
  +
pdb2gmx, then select: 1=AMBER03, 8=CHARMM27, 14=OPLS-AA/L:
 
 
/opt/SS12-Practical/gromacs/bin/pdb2gmx -f output/2nt0_A_1_re_sc.pdb -o output/2nt0_A_1.gro -p output/2nt0_A_1.top -water tip3p -ff amber03
+
/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

Latest revision as of 22:37, 25 June 2012

Sources

You can checkout the git repository containing all relevant data an scripts by:

git clone /mnt/home/student/angermue/mp/tasks/task07

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, 8=CHARMM27, 14=OPLS-AA/L:

 /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