Difference between revisions of "Gaucher Task07 Protocol"
From Bioinformatikpedia
(Created page with "== SCWRL == <pre> scwrl -i 2nt0_A.pdb -s 2nt0_A_1.seq -o 2nt0_A_1.pdb > 2nt0_A_1.out </pre> == FoldX == <tt>list.txt</tt> <pre> 2nt0_A.pdb </pre> <tt>mutant_list.txt:</tt> <pre…") |
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foldx -runfile run.txt |
foldx -runfile run.txt |
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+ | == Gromacs == |
Revision as of 08:50, 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