Sun Oct 9 04:40:55 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 Sun Oct 9 2011 at 04:40:55 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6529354 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 0.6529354 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 378.1387 centred at (gu) : 89.98240 89.94035 90.03505 assigned negative charge : -371.6396 centred at (gu) : 90.09805 89.85583 89.99167 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7339 nv = 96 ne = 84 npr = 51284 no. pairs analyzed = 51284 no. exposed pairs = 3400 no. arc points = 23929 no. surface atoms = 1147 nbur = 1394 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 3827 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8693 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7225780E-09 2.0616231E-08 midg,1,midg; midg,igrid,midg 1.7386653E-10 2.6543821E-08 1,midg,midg; igrid,midg,midg 3.1802429E-08 -4.8180784E-09 gauss-seidel spectral radius is 0.9878442 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 04:40:55 rms-change max change #iterations 0.1585927 25.19704 at 10iterations 1.6560033E-02 2.473907 at 20iterations 1.7674513E-03 0.2635574 at 30iterations 2.5012461E-04 3.4266472E-02 at 40iterations 6.7508256E-05 8.7699890E-03 at 50iterations finished qdiffx linear iterations at : 04:40:58 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 6.7508256E-05 8.7699890E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 04:40:59 3.335u 0.203s 0:03.85 91.6% 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 Sun Oct 9 2011 at 04:40:59 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.958806 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 1.958806 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 378.1387 centred at (gu) : 89.94677 89.82030 90.10429 assigned negative charge : -371.6396 centred at (gu) : 90.29405 89.56748 89.97480 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23929 grid for indexing accessible points = 1.400000 m= 28440 mr = 53640 m= 4731 mr = 20026 m= 350 mr = 2706 m= 8 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 36002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18982 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) : 0.6529354 object centre at (A) : 12.47900 27.20750 0.9235001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5853042E-03 2.8011836E-03 midg,1,midg; midg,igrid,midg 6.5350677E-03 4.0037774E-02 1,midg,midg; igrid,midg,midg 3.2066971E-02 -6.5345238E-03 gauss-seidel spectral radius is 0.9987094 estimated iterations to convergence 220 setup time was (sec) 0.8800000 now iterating at: 04:41:00 rms-change max change #iterations 4.435314 185.4696 at 10iterations 2.120348 77.54600 at 20iterations 1.018742 30.81527 at 30iterations 0.4874944 15.44026 at 40iterations 0.2345882 7.760391 at 50iterations 0.1122761 3.337436 at 60iterations 5.3843066E-02 1.740151 at 70iterations 2.5734048E-02 0.9401546 at 80iterations 1.2359382E-02 0.3725739 at 90iterations 5.9141535E-03 0.1978526 at 100iterations 2.8470291E-03 8.7730408E-02 at 110iterations 1.3737065E-03 4.0809631E-02 at 120iterations finished qdiffx linear iterations at : 04:41:07 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.3737065E-03 4.0809631E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 04:41:07 7.897u 0.239s 0:08.40 96.6% 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 Sun Oct 9 2011 at 04:41:07 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.938210 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 2.938210 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 378.1387 centred at (gu) : 89.92002 89.73035 90.15632 assigned negative charge : -371.6396 centred at (gu) : 90.44108 89.35121 89.96218 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 182297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23929 grid for indexing accessible points = 1.400000 m= 91576 mr = 130355 m= 33560 mr = 73198 m= 8409 mr = 25930 m= 1286 mr = 5805 m= 132 mr = 792 m= 5 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 81131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19215 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) : 1.958806 object centre at (A) : 12.47900 27.20750 0.9235001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2038697 0.1113381 midg,1,midg; midg,igrid,midg 5.7112999E-02 0.5185869 1,midg,midg; igrid,midg,midg 0.3037601 -7.8224987E-02 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.760000 now iterating at: 04:41:09 rms-change max change #iterations 10.47218 480.8821 at 10iterations 6.242712 160.6496 at 20iterations 3.702941 82.25573 at 30iterations 2.187424 47.49471 at 40iterations 1.285402 26.53286 at 50iterations 0.7546858 17.45198 at 60iterations 0.4420632 8.789301 at 70iterations 0.2587095 5.223100 at 80iterations 0.1509349 2.734426 at 90iterations 8.8068262E-02 1.634784 at 100iterations 5.1360216E-02 0.9708824 at 110iterations 2.9919736E-02 0.5541706 at 120iterations 1.7428249E-02 0.3349523 at 130iterations 1.0131007E-02 0.2098846 at 140iterations 5.8951867E-03 0.1091537 at 150iterations 3.4380783E-03 6.0522079E-02 at 160iterations 1.9986131E-03 3.5507202E-02 at 170iterations 1.1660891E-03 2.2293091E-02 at 180iterations finished qdiffx linear iterations at : 04:41:20 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.1660891E-03 2.2293091E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 04:41:21 13.123u 0.262s 0:13.71 97.5% 0+0k 0+0io 0pf+0w