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
 
</pre>
 
</pre>
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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

Gromacs