FUによるPSⅡの構造モデリング実習テキスト

1. FU PS28Apr2014) PDB X PDB (3arc.pdb) ps2 PDB (pro(chm)(wat) pro chm wat ) prochmwat ( ps2 TINKER ) GAMESS ) ps2 OEC A PDB B C FU D

2. 10 QM/MM fu-28Apr2014 ... FU (Windows7 32bit mode ) C:doc 1 fu-UsersGuide-ver0.1.1.pdf fumodel futools -28Apr2014.pdf futools ps2 ... C: ps2-example ps2-material ... ps2 ps2-example ... FU PS.pdf ps2-material ./pdb-data ... PDB ps2 PDB ( pdbxxx.ent ./oec-models batista-oec-2011 ... Batista OEC neese-oec-2012 ... Neese OEC siegbahn-oec-2013 ... Siegbahn OEC ./mhtfiles ... ps2-example 3arc.pdb ... ps2 pdb (./pdb-data/pdb3arc.ent C:c:ps2 rename 3. ps2 PDB http://pdbj.org/ 3arc.pdb ) c:/ps2/3arc c:/ps2/3arca ps2-material/pdb-data/pdb3arc.ent 3arc.pdb ps2 c: fumodel(32 3arc.pdb PyMol ps2 3arc.pdb Missing chains, resdiues and atoms) 1 PDB MISSING RESIDUES REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE ( REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 ( REMARK 610 MISSING HETEROATOM ( REMARK 610 LMG A 751 3arc.pdb UNL HET OEX A 601 10 ( HET UNL A 763 28 HET UNL A 748 16 ( 4. HETNAM FORMUL ps2 20 (Ca Sr 4il6.pdb 20 4il6.pdb OEC OEC ( futools report_unique_res 2 PDB HETEROGEN REMARK 600 HETEROGEN REMARK 600 ABOUT UNL A 763, C 745, D 723, a 763, d 723, k 745, THEY HAVE REMARK 600 CHARACTERISTIC THE ELECTRON DENSITY MAP AS SOME KIND OF REMARK 600 DIGLYCERIDES. 3 PDB HETNAM HETNAM OEX CA-MN4-O5 CLUSTER HETNAM FE2 FE (II) ION HETNAM CL CHLORIDE ION HETNAM BCT BICARBONATE ION ( 5. 4 report_unique_res executing program report_unique_res +++ enter file name of input PDB data c:ps23arc3arc.pdb +++ enter 1:AA, 2:Non-AA, or 3:all kind residues 3 report residues: all kind residues --- report-unique-res job starts at 2014/04/25 21:13:12 running ... number of total and unique residues 8368 40 residue list [[' CA', 7], [' CL', 6], [' MG', 2], ['ALA', 464], ['ARG', 226], ( UNL 38 PDB ftp .mht) FTP site of PDB: ftp://ftp.wwpdb.org/pub/pdb/data/monomers/ ps2-materialmhtfiles fumodel make_filelst_file futools tools misc mhtfiles.fuf 6. 5 make_filelst_file executing program make_filelst_file +++ enter directory name c:ps2ps2-materialmhtfiles +++ input file extension, like .pdb,... .mht +++ input special character for priority, '','@','!','$','%' +++ enter file name of filelst-file c:ps2mhtfiles.fuf --- make_filelst_file job starts at 2014/04/16 10:48:09 running ... ( +++ enter command for make_filelst_file, 1:quit, 2:again, 3:imode 1 quit make_filelst_file report_missing_atomsnon-aa residue option) Enter 7. 6 report_missing_atoms executing program report_missing_atoms +++ select job option. 1:non-aa residues, 2:aa-residues. 1 +++ enter file name of pdb file(.pdb) c:ps23arc3arc.pdb +++ input mht file(s). i.e. "file1,.." or "< file-lst file" (do not type quotes) < c:ps2mhtfiles.fuf +++ do you want to output in log file? 1:yes, 2:no 2 missing atoms: resnam, number of missing atoms and atmnam list (heavy atom only) ( BCR:649:B 0 SQD:768:D, 11, [' C21', ' C20', ' C22', ' C18', ' C19', ' C14', ' C15', ' C16', ' C17', ' C12', ' C13'] SQD:768:D( 11 SDQ:667:a report_missing_atoms(aa-residues option) N C 8. ps2 chain a b 2 (A,B,C,D) PDB split_pdb chain option 3arc.pdb chain PDB 3arc-chain.spl chain c:ps23arca3arca.mrg 7 split_pdb executing program split_pdb +++ select split option. 1: at TER, 2:chains, 3: pro,chm,wat 2 split option: chains +++ enter file name of input pdb file c:ps23arc3arc.pdb +++ enter directory name of output PDB files c:ps23arcchain directory not found. directory name= c:ps23arcchain +++ do you want to re-enter or create? 1:re-enter, 2:create, 3:quit the job 2 +++ do you want to output in log file? 1:yes, 2:no 2 base name of created pdb files= 3arc ( --- split_pdb job ends at 2014/04/15 10:01:50, elapsed time: 1 sec. 9. 8 3arc-chain.spl # created by split_pdb at 2014/04/15 10:01:50 # parent pdb filec:ps23arc3arc.pdb c:ps23arcchain3arc-uA.pdb #A -3467 c:ps23arcchain3arc-uB.pdb #B -5786 c:ps23arcchain3arc-uZ.pdb #Z -534 c:ps23arcchain3arc-la.pdb #a -3409 c:ps23arcchain3arc-lb.pdb #b -5666 c:ps23arcchain3arc-lz.pdb #z -519 merge_pdb 3arca.mrg a PDB c:ps23arca3arca.pdb fumodel (fumodel 32 5 split_pdb (pro,chm,wat option, no environment)3arca.pdb 3arca-pro.pdb3arca-chm.pdb3arca-wat.pdb c:ps23arcapro-chm-wat chain c:/ps2/3arca/3 arca.mrg 9 merge_pdb executing program merge_pdb +++ input pdb files to be merged. i.e. "file1,.." or "< file-lst file" (do not type quotes) < c:ps23arca3arca.mrg +++ enter file name of output pdb file(full path) c:ps23arca3arca.pdb --- merge_pdb job starts at 2014/04/25 21:26:13 running ... total number of atoms 27140 --- merge_pdb job ends at 2014/04/25 21:26:14, elapsed time: 1 sec. 10. 10 split_pdb executing program split_pdb +++ select split option. 1: at TER, 2:chains, 3: pro,chm,wat 3 split option: into pro,chm,wat +++ enter file name of input pdb file c:ps23arca3arca.pdb +++ enter directory name of output PDB files c:ps23arcapro-chm-wat directory not found. directory name= c:ps23arcapro-chm-wat +++ do you want to re-enter or create? 1:re-enter, 2:create, 3:quit the job 2 +++ do you want to output in log file? 1:yes, 2:no 2 ( split-fileslst file is created c:ps13arcaprochmwat3arca-pro-chm-wat.spl number of created split files= 3 pro 3arca-pro.pdb split-pdb(chain chain c:/ps2/3arca/pro-chm-wat/pro-chain 11. +++ enter command...35 12 futoolsfumodel +++ enter command for split_pdb, 1:quit, 2:again, 3:imode 3 +++ >>> 1:quit, 2:again, 3:view input pdb, 4:view output pdb, 5:view pdb(&frg) in directory. 5 openning fumodel ... ( fumodel PDB chain 19 Molecule >Add-H and bond to AA residue ( Default PDB @3arca-pro-uA.pdb -> [email protected] close futools (@ make_files_file 11 split_pdb executing program split_pdb +++ select split option. 1: at TER, 2:chains, 3: pro,chm,wat 2 split option: chains +++ enter file name of input pdb file c:ps23arcapro-chm-wat3arca-pro.pdb +++ enter directory name of output PDB files c:ps23arcapro-chm-watpro-chain ( split-fileslst file is created c:ps23arcapro-chm-watpro-chain3arca-pro-chain.spl number of created split files= 19 --- split_pdb job ends at 2014/04/26 17:04:01, elapsed time: 3 sec. 12. 1 fumodel close ( 19 fumodel script c:ps2fu-script script PyCrust >>> fum.ExecuteScript1(c://ps2//fu-script//add_h_to_pro.py) add_h_to_pro.py 19 PDB 2 PyCrust (// ( script (fumodel fum script method 2 ExecuteScript ExecuteScript1( script Script scrpit split_pdb make_filelst_file merge_pdb @ c:/ps2/3arca/pro-chm-wat/[email protected] 13. 13 make_filelst_file executing program make_filelst_file +++ enter Directory name c:ps23arcapro-chm-watpro-chain +++ input file extension, i.e. .pdb,... .pdb +++ input priority character at the end of base name, '','@','!','$','%' @ +++ enter file name of filelst-file c:[email protected] --- make_filelst_file job starts at 2014/04/26 17:14:06 running ... searched files with extension, .pdb, in directory c:ps23arcapro-chm-watpro-chain number files found: 38 number of picked up files with special character, @ = 19 c:[email protected] file is created. number of files: 19 --- make_filelst_file job ends at 2014/04/26 17:14:06, elapsed time: 0 sec. merge_pdb pro [email protected] 14 merge_pdb executing program merge_pdb +++ input pdb files to be merged. i.e. "file1,.." or "< file-lst file" (do not type quotes) < c:[email protected] +++ enter file name of output pdb file(full path) c:[email protected] --- merge_pdb job starts at 2014/04/26 17:15:49 running ... total number of atoms 41116 --- merge_pdb job ends at 2014/04/26 17:15:51, elapsed time: 2 sec. fumodel [email protected] Select-Non-bonded atom ( 14. 3 3arca-pro.pdb LEU:40:J, LEU46:Y, ALG:45:F, LEU:352:D, LYS:84:E fumodel 3arca-pro.pdb (c:/ps2/3arca/pro-chm-wat Add-H and bond to AA residue fumodel fumodelset.py ,fum.usefmoutil=True(default) Fortran False python 30 chm fumodel File-Open 3arca-chm.pdb mhtfiles.fuf (fu-23Dec2013 mht file Add-H and bond to non-AA residue-Use frame data ( 4 non-bonded 15. (SelObject-residue L-Click tree selector residue Show-Selected only, f 5 HTG:726:D, DGD:660:C, DGD:657:C, LMG:751:A, SQD:768:D, LMG:784:Z, DGD:755:D, LHG:772:E, LMG:729:C, LMG:776:C, LMG:669:B, DGD:661:C, LMG:692:D, DGD:663:H L-Click Add-functional group Del-Selected( Delete / DGD LMG 2 6 UNL.mht Select-Selector-Name/Number Residue UNL 16. 7 UNL) Add-H and bond to non-aa residue-Use bond length 8 / 3arca-chm.pdb ( Add-H and bond to non-AA residue-Use frame data Add-H and bond to non-AA residue-Use bond length 3arca-chm.pdb [email protected] script PyCrust >>> fum.ExecuteScript1(c://fu-script//add_h_to_chm.py) wat 17. fumodel 3arca-wat.pdb Add-H and bond to water H [email protected] H prochmwat [email protected] [email protected] make_files_file merge_pdb c:/ps2/3arca/[email protected] (fumdodel File-Merge PDB GUI HIS) HIS (54 HIS ( HIS pick_up_obj [email protected] HIS 18. 15 pick_up_obj eexecuting program pick_up_obj +++ input object name, i.e. "ALA", "chm", "pro"(do not type quotes). HIS +++ with environment? 1:no, 2: yes, 3:quit 2 +++ input cut-off distance(in A) of environment. 4 +++ enter file name of input pdb file c:[email protected] +++ enter directory name of output PDB files c:ps23arca3arca@his-e40 directory not found. directory name= c:ps23arca3arca@his-e40 +++ do you want to re-enter or create? 1:re-enter, 2:create, 3:quit the job 2 --- pick_up_obj job starts at 2014/04/26 17:47:58 ( number of atoms in picked-up residue= 259 number of created PDB files= 54 split fileslst file is created c:ps23arca3arca@[email protected] --- pick_up_obj job ends at 2014/04/26 17:48:17, elapsed time: 18 sec. +++ enter command for pick_up_obj, 1:quit, 2:again, 3:imode 3 +++ >>> 1:quit, 2:again, 3:view input pdb, 4:view output pdb, 5:view pdb(&frg) in directory. 5 ( fumodel 54 HIS 4 PDB 19. Molecule HIS Delete" Del-Selected Save as PDB @ [email protected] 10 Molecule Add-Bond 11 MG H Molecule SelObjectSelMode 9 MusMode Mouse mode 20. 12 PDB HIS make_filelst_file c:/ps2/3arca/3arca@/his-e40 PDB base @ c:/ps2/3arca/3arca@/his-e40/[email protected] replace_res c:/ps2/3arca/[email protected] HIS c:/ps2/3arca/3arca@@.pdb 16 replace_res executing program replace_res +++ enter file name of input target pdb file c:[email protected] +++ input residue pdb file(s) < c:ps23arca3arca@[email protected] +++ enter file name of output pdb files c:ps23arca3arca@@.pdb --- replace_res job starts at 2014/04/26 18:52:55 running ... resnam,resnmb,chain in ReplaceRes HIS 100 B ( note: connect data were recreated based on distance. --- replace_res job ends at 2014/04/26 18:53:04, elapsed time: 9 sec. fumodel 3arca@@.pdb Select-Selectore-Name/Number residue HIS Show-Selected only HIS HIS a (c:/ps2/3arca/3arca@@.pdb) 21. (54 HIS script CLA MG HIS 18 HIS c:3arcafu-scripthis_delete_h.py fumodel PyCrust >>> fum.ExecuteScript1(c://ps2//fu-script//his_delete_h.py) 18 ( script [email protected] fumodel @ ( fumodel 3arca@@.pdb Add-box water (32bit FU shell(3.5) 3arca@@-w35.pdb 13 ( 300K MD FU datawater-box.pdb ) Amber MD FU TINKER AMBER GROMACS 22. 3arc.pdb OEC PCM ps2 missing atoms icheck_geom 3arca-chm@@.pdb 23. 17 check_geom executing program check_geom ! this program requres pdb file with connect data. +++ select check option. 1:bond length, 2:angle, 3:vdW contact, 4:quit. 1 threshold length should be give by factors:fmin and fmax for r < fmin*r0, r> fmax*r0 (r0:standard single bond length). +++ input fmin and fmax, like "0.8 1.2" (" is not input data). find bond whose distance is shorter than 0.8 or longer than 1.2 times of standard value +++ enter file name of pdb file(.pdb) c:ps23arca3arca@@.pdb +++ do you want to output in log file? 1:yes, 2:no 1 job may take several minutes for 10,000 atoms. --- check_geom job starts at 2014/04/15 16:47:07 running ... total number of bond length parameters= 11704 number of wrong length bonds= 55 number rij i-atom j-atom i-atmnam j-atmnam i-resnam j-resnam 1 1.205 725 743 C11 C12 BCR:A BCR:A 2 1.199 748 750 C15 C16 BCR:A BCR:A ( 55 1.202 10960 10962 C20 C21 BCR:T BCR:T ( C-C BCR2 angle option 90 OEC CLA BCR:651:D C29-C30-C39 88.7 ii) fumodel iii)UNL) 24. fumodel iv)fumodel Add-Bond-Hydrogen bond 14 MOab initio semi-emprical FMO) FMO PIE FMO-RHF/STO-3G BCR:651:D AM1 i)c:/ps2/3arca/pro-chm-wat extract ii)extract_res 3arca@@.pdb BCR:651:D 25. 18 extract_res executing program extract_res +++ input resdiue data in full form, like "ALA:1:A"(do not type quotes) BCR:651:D +++ with environment? 1:no, 2:yes, 3:quit 1 +++ enter file name of input pdb file c:ps23arca3arca@@.pdb +++ enter file name of output pdb files c:[email protected] --- extract_res job starts at 2014/04/26 19:03:07 running ... extracted residues: ['BCR:651:D'] number of atoms in extracted residue= 96 --- extract_res job ends at 2014/04/26 19:03:08, elapsed time: 1 sec. iii) PDB fumodel Add-Bond-Usebond length MO C29-C30-C39 iv)Script GAMESS assist.py GAMESS assistant Run type energy AM1 AM1 Make input Edit/View GAMESS input file input file $basis GBASIS=AM1 $end $contrl ichrag=) mult=) fumodel 26. 19 GAMESS AM1 ! Created by fu at 2014/04/17 07:55:07 $contrl runtyp=energy ispher=1 nprint=-5 $end $system mwords=115 $end $scf dirscf=.t. npunch=0 $end $basis GBASIS=AM1 $end $data SQD768uD-e0-o C1 1 6 9.663000 -80.917000 178.790000 2 1 10.094000 -79.890000 178.929000 ( v)RunGAMESS AM1 15 AM1 1 30 iteration extract_res PDB split_pdb python script 7-2) fumodel Change-Charge FMO-Fragment tools-Charge assign PDB '.xyz' 27. ps2 ps2 / AM1 ab initio FMO AM c:/ps2/3arca/pro-chm-wat/pro-chain [email protected] fumodel PDB Script tinker_optimize.py TINKER Optimization RMS gradient convergence 5 kcal/mol/ Exec (fumodel PyCrust TINKER 16 TINKER Overlay Update File-Save as c:[email protected] replace_res 3arca@@.pdb 28. 20 replace_res executing program replace_res +++ enter file name of input target pdb file c:ps23arca3arca@@.pdb +++ input residue pdb file(s) c:[email protected] +++ enter file name of output pdb files c:ps23arca3arca-pro@@-o.pdb --- replace_res job starts at 2014/04/15 18:30:15 ( +++ enter command for replace_res, 1:quit, 2:again, 3:imode 1 quit replace_res SQD:768:D SQD:668:B transfer UNL transfer OEC reference extract_res 3arca@@.pdb SQD:768:D SQD:668:B extract fumodel target SQD768D.pdb Add-Bond-Use bond length Script transfer_atoms.py tranfer_atoms.py Read SQD668uB.pdb fMusMod translate CTRL R-Drag target (fumodel CTRLR-Drag target C7,C8,C9,C10,C11 L-Cick SelMod multiSelObject atom reference selObjct group L-Click 29. Transfer_atoms matching atom name (resnam resnmb Apply RMS fit Do reference target Select atom Apply Reference molecule Del reference 17 C11 C12 2.21Show-Distance L-Click C12 C22 CTRL R-Drag 1.54 (MusMode translate 18 SQD mht fileSQD.mht Script GAMESS-assist.py Runtype optimize Make input Edit/View input data AM1 $statpt opttol=0.01 RunGAMESS 30. 19 AM1 Change-Update coordinate from file File-Save as c:ps23arcapro-chm-watextractSQD768D-o.pdb replace_res 3arca@@.pdb (. 20 ( (fumodel Change-Conformation Z-Matrix editor 2 File-Merge rms fit Script rms_fit.py transfer-atoms.py ps2 31. ps2 ()FU AM1AM1LJ FMO [email protected] extract_res with environment option) residue **:F' fumodel File-Open Add-Bond-Bondlength Add-H to cut AA chain F select Script tinker_optomize.py RMS gradient 1kcal/A Overly Update [email protected] 21 TINKER ( 22 -715.5719 1.6957 2.4148 0.1492 319 TruncNewt 306 23 -718.1711 0.9632 2.5992 0.0712 333 TruncNewt 323 TNCG -- Normal Termination due to SmallGrad Final Function Value : -718.1711 Final RMS Gradient : 0.9632 Final Gradient Norm : 22.7946 ... e:tinker-6.2.06bin-win64/newton.exe ended at 2014/04/16 18:36:36 ... elapsed time= 28.58 (sec) 32. 21 rms fit(RMSD=0.894 replace_res 3arca@@.pdb HTG698B ) HTG Script GAMESS_assist.py Runtype optimize Makeinput Edit/View input file $contrl icharg=-1, $statpt opttol=0.01, $basis GBASIS=AM1 $end RunGAMESS GAMESS 22 GAMESS 33. GAMESS HTG698uB-e5.inpHTG698uB-e5.out (PDB .inp .out ChangeUpdate coordinates from file StatusBar deviation between old and new coordinates=0.0053 A ( RMS fit Save as HTG698B-e5-o.pdb replace_res 3arca@@.pdb (fumodel script make_am1_input.py (c:/ps2/fu-script 3arc@@.pdb pick_up_obj (residues, with envorinment option) c:ps23arca@@chm-res-e50 residue c:ps23arca@@chm-res-e503arca@@-res.spl PyCrust > fum.ExecuteScript1(c://ps2//fu-script//make_am1_input.py) xxx.inp GAMESS Windows xxx.bat GAMESS script dat='rungms '+inpfile+' 13-64 1 0 '+outfile+'n' ( 3arca@@.pdb fumodel 22 GAMESS MAXIMUM GRADIENT = 0.0087992 RMS GRADIENT = 0.0011381 NSERCH: 15 E= -1434.1968347733 GRAD. MAX= 0.0087992 R.M.S.= 0.0011381 ***** EQUILIBRIUM GEOMETRY LOCATED ***** ( .....END OF GEOMETRY SEARCH...... CPU 0: STEP CPU TIME= 6.60 TOTAL CPU TIME= 344.0 ( 5.7 MIN) TOTAL WALL CLOCK TIME= 344.0 SECONDS, CPU UTILIZATION IS 100.00% 34. Change-Charge FMO script 10 QM exa MM AM1 OEC ab initio microiteration optimization FMO frozen domain FMO/FD, D.G.Fedorov et al.,J. Phys. Chem. Lett., 2, 282 (2011)) microiteration optimization extract_res(with environment option) futools fumodel 1 fumodel fumodel OEC ps2 OEC OEC fumodel OEC OEC 5 transfer OEC 2 OEC c:/ps2/neese-oec-model/OEX601A-e50.pdb OEX-e50 35. Neese OEC F.Neese OEC PDB ( c:/ps2/ps2-material/oec-models/neese-oec-2012/neese-structure-a.xyz Dimitrios A. et al., Angew. Chem. Int. Ed. 2012, 51, 9935, SI:Optimized Cartesian Coordinates Structure A)fumodel Add-bond-Use bond length File-Save as c:ps2neese-oec-modelnesse-structure-a.pdb (OEX-neese PDB OEC 23 extract_res e executing program extract_res +++ input resdiue data in full form, like "ALA:1:A"(do not type quotes) OEX:601:A +++ with environment? 1:no, 2:yes, 3:quit 2 +++ input cut-off distance(A) of environment. 5 +++ enter file name of input pdb file c:ps23arca3arca@@.pdb +++ enter file name of output pdb files c:ps2neese-oec-modelOEXA-e50.pdb --- extract_res job starts at 2014/04/26 19:11:22 running ... extracted residues: ['OEX:601:A'] cut off distance of environmental resiue= 5.0 emvironmental residues: ['ASP:61:A', 'ASN:87:A', 'TYR:161:A', ( 36. 24 OCEPDB REMARK Created by fu at 2014/03/20 21:21:43 HETATM 1 MN1 -1 -24.871 -35.533 203.969 0.00 0.00 MN 0 HETATM 2 MN2 -1 -27.359 -35.264 205.245 0.00 0.00 MN 0 HETATM 3 MN3 -1 -27.348 -33.371 203.184 0.00 0.00 MN 0 HETATM 4 MN4 -1 -27.606 -33.205 200.442 0.00 0.00 MN 0 HETATM 5 CA1 -1 -27.875 -36.772 202.211 0.00 0.00 CA 0 HETATM 6 O1 -1 -26.431 -36.528 204.227 0.00 0.00 O 0 HETATM 7 O2 -1 -28.376 -34.764 203.816 0.00 0.00 O 0 ( File-Open OEX601A-e50.pdb Script rms-fit.py Reference molecule: Read OEX-neese OEC rms fit OEX-neese OEX OEX601A-e50.pdb PDB Select-Select All RMS Fitting maiching parameter atom names Matting atoms: Apply RMS fit Fit replace_res neese OEX transfer Add-Add H to cut AA OEX c:ps2neese-oec-modelneese-structure-a-e50.pdb OEC OEX SelObject atomSelMode dual 2 1 Neese OEC fumodel OEC 37. FU 3 ps2 FU 2 mht pro fumodel 3arca.pdb [email protected] HIS [email protected] his_delete_h.py HIS 3arca@@.pdb " 1 FU 38. A PDB split_pdb pro-chm-wat option PDB -pro.pdb, -chm.pdb, -wat.pdb 3arca-pro.pdb) split_pdb chain option PDB -chain .pdb chain uA, la (3arc-uA.pdb) split_pdb resdiue option PDB - + -chain 3arca-chm-SQD668-uB.pdb) split_pdb unique residue option PDB -.pdb)3arca-chm-SQD.pdb B chain (3 1 5 (SQD:768:D SQD:*:* (* SQD C FU .pdb ... PDB file .ent ... PDB file .xyz ... FU Cartesian GAMESS GAMESS-FMO Cartesian .tin ... TINKER xyz file .mht ... .fuf ... fumodel (.pdb, .mht, .frg.bda ) format .spl .mrg .frg ... fragment data file .bda ... bda data file 3arc.pdb 3arca.pdb 3arca-pro.pdb 3arca-chm.pdb 3arca-wat.pdb monomer 39. .inp ... GAMESS input file .out ... GAMESS output file .log ... futools pdb log file.session log .fub ... futools .spl ... split_pdb PDB file .mrg ... merge_pdb .spl format D FU 40. c:/ps2 |___./ps2-material | |___./pdb-data | | |___ pdb3arc.ent | | |___ ... | |___./mhtfiles | | |___BCR.mht | | |___ ... | |___./oec-models | |___./batista-oec-2011 | | |___ ... | |___./nesse-oec-2012 | | |___ ... | |___./seigbarn-oec-2013 | |___ ... |___./fu-script | |___his_delete_h.py | |___make_am1_input.py | |___add_h_to_pro.py | |___add_h_to_chm.py |___mhtfiles.fuf |___./3arc | |___3arc.pdb | |___./chain | |___3arc-chinxxx.pdb | |___ ... | |___3arc-chain.spl |___./neese-oec-model | |___neese-structure-a-e50.pdb | |___ ... ps2 41. |___./3arca |___3arca.pdb |___3arca.mrg |___./pro-chm-wat | |___./extract | | |___ ... | |___./pro-chain | | |___3arca-pro-xxx.pdb | | |___ ... | |___3arca-pro.pdb | |___3arca-chm.pdb | |___3arca-wat.pdb |___./3arca@ | |___./his-e40 | |___ ... |[email protected] |[email protected] |___3arca@@.pdb |___./3arca@@ | |___./chm-res-e50 | |___xxx.pdb | |___xxx.inp | |___ ... |___3arca@@-wat35.pdb

FUによるPSⅡの構造モデリング実習テキスト

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Transcript of FUによるPSⅡの構造モデリング実習テキスト