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Copy pathexample-docking-input.txt
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example-docking-input.txt
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READ FFIELD params/amber99sb-est.prm
READ DEFS params/defs-amber99sb-est.txt
INSERT SEQUENCE
LEUN ALA LEU SER LEU THR ALA ASP GLN MET VAL SER ALA LEU LEU ASP ALA GLU PRO PRO
ILE LEU TYR SER GLU TYR ASP PRO THR ARG PRO PHE SER GLU ALA SER MET MET GLY LEU
LEU THR ASN LEU ALA ASP ARG GLU LEU VAL HIE MET ILE ASN TRP ALA LYS ARG VAL PRO
GLY PHE VAL ASP LEU THR LEU HIE ASP GLN VAL HIP LEU LEU GLU CYS ALA TRP LEU GLU
ILE LEU MET ILE GLY LEU VAL TRP ARG SER MET GLU HIE PRO GLY LYS LEU LEU PHE ALA
PRO ASN LEU LEU LEU ASP ARG ASN GLN GLY LYS CYS VAL GLU GLY MET VAL GLU ILE PHE
ASP MET LEU LEU ALA THR SER SER ARG PHE ARG MET MET ASN LEU GLN GLY GLU GLU PHE
VAL CYS LEU LYS SER ILE ILE LEU LEU ASN SER GLY VAL TYR THR PHE LEU SER SER THR
LEU LYS SER LEU GLU GLU LYS ASP HIP ILE HIE ARG VAL LEU ASP LYS ILE THR ASP THR
LEU ILE HIE LEU MET ALA LYS ALA GLY LEU THR LEU GLN GLN GLN HIE GLN ARG LEU ALA
GLN LEU LEU LEU ILE LEU SER HIE ILE ARG HIE MET SER ASN LYS GLY MET GLU HIE LEU
TYR SER MET LYS CYS LYS ASN VAL VAL PRO LEU TYR ASP LEU LEU LEU GLU MET LEU ASP
ALA HIP ARGC
END
INSERT LIGAND est
#helix 12, plus all AA's with at least one heavy atom within 3 A of the ligand in any reference -- 36 total
AAREGION 38,41-42,45-46,48,79,82-83,86,89,99,114,116,119-120,123,216,219-220,228-243
READ PDB data/er-active-hie219-est.pdb
SEDDD 2.0 8.0 0.625 0.000001 params/solvpar-seddd-est.txt
CUTOFF 10.0 10.0
GO_MODEL
HARDCORE 1.7
NATIVE_CUTOFF 8.0
EXPONENTS 12 10
WELLDEPTH 3.0
NATIVE_STATE data/er-active-hie219-est.pdb
END
MOVES
backbone 0.1 2.0
sidechain 0.2 180.0
backrub 0.1 2.0
ligand-bond 0.2 180.0
ligand-trans 0.2 0.1 1.0 2.0
ligand-rot 0.2 1.0 1.0 180.0
heavy-atom-trans 0.0 0.1
heavy-atom-rot 0.0 30.0
end
TEMP 300.0
WRITE PSF psf/er-active-hie219-est-1-cutoff3allref-movemix10.psf
SAVEFREQ 100
PRINTFREQ 100
TRAJ DCD dcd/er-active-hie219-est-1-cutoff3allref-movemix10.dcd
SETLIGANDCOM 105.04141998291016 14.675309181213379 23.48505973815918
WRITE PDB data/er-active-hie219-est-1-cutoff3allref-movemix10-start.pdb
DOCKPREP 4.0 180.0 1000
WRITE PDB data/er-active-hie219-est-1-cutoff3allref-movemix10-init.pdb
MCLOG mcinfo/mc-log-active-hie219-est-1-cutoff3allref-movemix10
RUN 30000
WRITE MCBYATOM mcinfo/mc-byatom-active-hie219-est-1-cutoff3allref-movemix10
ENERGY LIGAND