Difference between revisions of "Gaucher Task07 Protocol"
From Bioinformatikpedia
(→Gromacs) |
(→Gromacs) |
||
Line 68: | Line 68: | ||
/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 output/2nt0_A_1_re.pdb -o output/2nt0_A_1_re_sc.pdb |
||
+ | |||
+ | repairPDB again: |
||
+ | |||
+ | /opt/SS12-Practical/scripts/repairPDB output/2nt0_A_1_re_sc.pdb -jprot > output/2nt0_A_1.pdb |
||
pdb2gmx: |
pdb2gmx: |
||
− | /opt/SS12-Practical/gromacs/bin/pdb2gmx -f output/ |
+ | /opt/SS12-Practical/gromacs/bin/pdb2gmx -f output/2nt0_A_1.pdb -o output/2nt0_A_1.gro -p output/2nt0_A_1.top -water tip3p -ff amber03 |
Revision as of 09:51, 25 June 2012
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
Gromacs
repairPDB:
/opt/SS12-Practical/scripts/repairPDB 2nt0_A_1.pdb -jprot > output/2nt0_A_1_re.pdb
SCWRL:
/opt/SS12-Practical/scwrl4/Scwrl4 -i output/2nt0_A_1_re.pdb -o output/2nt0_A_1_re_sc.pdb
repairPDB again:
/opt/SS12-Practical/scripts/repairPDB output/2nt0_A_1_re_sc.pdb -jprot > output/2nt0_A_1.pdb
pdb2gmx:
/opt/SS12-Practical/gromacs/bin/pdb2gmx -f output/2nt0_A_1.pdb -o output/2nt0_A_1.gro -p output/2nt0_A_1.top -water tip3p -ff amber03