Mon Oct 10 14:04:57 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:04:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: GLM 276 has a net charge of -0.0940 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5514763 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -2.130000 50.52900 ymin,ymax (A): -10.58800 39.43700 zmin,zma (A): -16.95100 47.60300 x,y,z range (A): 52.65900 50.02500 64.55400 scale (grids/A): 0.5514763 object centre (A): 24.19950 14.42450 15.32600 number of atom coordinates read : 2742 total number of charged atoms : 2597 net assigned charge : 7.445015 assigned positive charge : 418.1635 centred at (gu) : 89.80090 91.18705 89.28580 assigned negative charge : -410.7195 centred at (gu) : 89.75388 91.02507 89.32806 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5368 nv = 96 ne = 84 npr = 54445 no. pairs analyzed = 54445 no. exposed pairs = 3613 no. arc points = 25494 no. surface atoms = 1210 nbur = 1532 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 224 mr = 2633 m= 0 mr = 8 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2563 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7014 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0370220E-09 2.0201238E-10 midg,1,midg; midg,igrid,midg -5.0552990E-10 2.3461313E-09 1,midg,midg; igrid,midg,midg 2.0903863E-10 8.6460988E-10 gauss-seidel spectral radius is 0.9830262 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 14:04:58 rms-change max change #iterations 7.4466944E-02 12.95953 at 10iterations 5.1291366E-03 0.9494400 at 20iterations 3.5110023E-04 6.0050964E-02 at 30iterations 2.4013285E-05 4.0493011E-03 at 40iterations 1.9141917E-06 3.1089783E-04 at 50iterations finished qdiffx linear iterations at : 14:05:02 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.9141917E-06 3.1089783E-04 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 14:05:03 4.677u 0.408s 0:05.58 90.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:05:03 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: GLM 276 has a net charge of -0.0940 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.654429 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -2.130000 50.52900 ymin,ymax (A): -10.58800 39.43700 zmin,zma (A): -16.95100 47.60300 x,y,z range (A): 52.65900 50.02500 64.55400 scale (grids/A): 1.654429 object centre (A): 24.19950 14.42450 15.32600 number of atom coordinates read : 2742 total number of charged atoms : 2597 net assigned charge : 7.445015 assigned positive charge : 418.1635 centred at (gu) : 89.40218 93.56046 87.85667 assigned negative charge : -410.7195 centred at (gu) : 89.26142 93.07507 87.98389 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18072 mr = 39113 m= 1882 mr = 11911 m= 59 mr = 830 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 27427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 332 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19936 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5514763 object centre at (A) : 24.19950 14.42450 15.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0311847E-02 1.4043957E-02 midg,1,midg; midg,igrid,midg 1.2467080E-03 1.3526783E-02 1,midg,midg; igrid,midg,midg -1.2633535E-02 7.0975715E-04 gauss-seidel spectral radius is 0.9982138 estimated iterations to convergence 188 setup time was (sec) 0.8300000 now iterating at: 14:05:04 rms-change max change #iterations 3.242973 180.1551 at 10iterations 1.357887 59.07009 at 20iterations 0.5690514 21.81948 at 30iterations 0.2386105 9.241333 at 40iterations 0.1000865 3.868324 at 50iterations 4.2070869E-02 1.541440 at 60iterations 1.7645091E-02 0.7201023 at 70iterations 7.4331174E-03 0.2541392 at 80iterations 3.1352404E-03 0.1231537 at 90iterations 1.3166874E-03 5.1452637E-02 at 100iterations 5.5725401E-04 2.0346642E-02 at 110iterations 2.3880457E-04 9.1025829E-03 at 120iterations finished qdiffx linear iterations at : 14:05:14 total time elapsed so far: 10.70000 # loops : 120 mean,max change (kT/e) : 2.3880457E-04 9.1025829E-03 energy calculations done at 10.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.89000 DelPhi exited at 14:05:15 10.890u 0.448s 0:11.66 97.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:05:15 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2742 !!! WARNING: HIR 183 has a net charge of 0.5140 !!! WARNING: GLM 276 has a net charge of -0.0940 !!! WARNING: SEP 329 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.481643 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -2.130000 50.52900 ymin,ymax (A): -10.58800 39.43700 zmin,zma (A): -16.95100 47.60300 x,y,z range (A): 52.65900 50.02500 64.55400 scale (grids/A): 2.481643 object centre (A): 24.19950 14.42450 15.32600 number of atom coordinates read : 2742 total number of charged atoms : 2597 net assigned charge : 7.445015 assigned positive charge : 418.1635 centred at (gu) : 89.10318 95.34068 86.78478 assigned negative charge : -410.7195 centred at (gu) : 88.89211 94.61237 86.97588 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 137808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 62620 mr = 96377 m= 17539 mr = 48326 m= 2871 mr = 12651 m= 257 mr = 1666 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 61983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20746 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.654429 object centre at (A) : 24.19950 14.42450 15.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6933232 0.2459505 midg,1,midg; midg,igrid,midg 3.6897998E-02 0.1411348 1,midg,midg; igrid,midg,midg -0.1867721 1.5091989E-02 gauss-seidel spectral radius is 0.9991419 estimated iterations to convergence 270 setup time was (sec) 1.590000 now iterating at: 14:05:17 rms-change max change #iterations 8.546596 494.4328 at 10iterations 4.858992 240.3272 at 20iterations 2.743921 68.72238 at 30iterations 1.538607 37.91609 at 40iterations 0.8593212 21.19567 at 50iterations 0.4783829 11.50935 at 60iterations 0.2656790 6.324333 at 70iterations 0.1472046 3.361334 at 80iterations 8.1593737E-02 1.947651 at 90iterations 4.5055032E-02 1.216640 at 100iterations 2.4859531E-02 0.6082077 at 110iterations 1.3718115E-02 0.2855110 at 120iterations 7.5728665E-03 0.1663094 at 130iterations 4.1789073E-03 8.5405350E-02 at 140iterations 2.3014199E-03 5.9451580E-02 at 150iterations 1.2685173E-03 2.6470661E-02 at 160iterations 6.9876574E-04 1.4995575E-02 at 170iterations 3.8668889E-04 9.4299316E-03 at 180iterations finished qdiffx linear iterations at : 14:05:34 total time elapsed so far: 18.64000 # loops : 180 mean,max change (kT/e) : 3.8668889E-04 9.4299316E-03 energy calculations done at 18.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.79000 DelPhi exited at 14:05:35 18.793u 0.514s 0:19.70 97.9% 0+0k 0+0io 0pf+0w