Sat Oct 15 14:34:56 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 Sat Oct 15 2011 at 14:34:56 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6207714 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 0.6207714 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.485975 assigned positive charge : 434.1121 centred at (gu) : 89.12690 89.59843 89.21045 assigned negative charge : -436.5992 centred at (gu) : 89.05212 89.53040 89.18875 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7517 nv = 96 ne = 84 npr = 57010 no. pairs analyzed = 57010 no. exposed pairs = 3783 no. arc points = 26454 no. surface atoms = 1274 nbur = 1593 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3979 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2000000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2899808E-09 -2.6383981E-10 midg,1,midg; midg,igrid,midg -7.8519884E-09 2.9226843E-09 1,midg,midg; igrid,midg,midg -9.3591970E-09 3.0394636E-09 gauss-seidel spectral radius is 0.9865925 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 14:34:57 rms-change max change #iterations 0.1323924 16.55988 at 10iterations 1.2312896E-02 1.970242 at 20iterations 1.1387536E-03 0.1632917 at 30iterations 1.0390224E-04 1.4099598E-02 at 40iterations 9.7775519E-06 1.4376640E-03 at 50iterations finished qdiffx linear iterations at : 14:35:04 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 9.7775519E-06 1.4376640E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:35:05 3.633u 0.200s 0:08.51 45.0% 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 Sat Oct 15 2011 at 14:35:05 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.862314 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 1.862314 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.485975 assigned positive charge : 434.1121 centred at (gu) : 87.37980 88.79423 87.63054 assigned negative charge : -436.5992 centred at (gu) : 87.15609 88.59118 87.56580 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26454 grid for indexing accessible points = 1.400000 m= 27696 mr = 55328 m= 3806 mr = 19666 m= 175 mr = 2081 m= 5 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1468 time to turn everything in is 0.3900000 number of dielectric boundary points 35846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21404 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) : 0.6207714 object centre at (A) : 20.01500 15.33600 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0909208E-02 5.6807883E-03 midg,1,midg; midg,igrid,midg -2.3284419E-02 -2.7564543E-04 1,midg,midg; igrid,midg,midg -4.7207616E-02 2.4044201E-02 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.6300000 now iterating at: 14:35:06 rms-change max change #iterations 4.323864 167.1265 at 10iterations 2.003628 76.26402 at 20iterations 0.9314678 35.22633 at 30iterations 0.4321329 12.84490 at 40iterations 0.2003032 6.464452 at 50iterations 9.2955001E-02 2.870233 at 60iterations 4.3187562E-02 1.542435 at 70iterations 2.0056823E-02 0.6772289 at 80iterations 9.3144737E-03 0.2840562 at 90iterations 4.3454771E-03 0.1518211 at 100iterations 2.0132391E-03 6.1687469E-02 at 110iterations 9.3800557E-04 3.0036926E-02 at 120iterations finished qdiffx linear iterations at : 14:35:21 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 9.3800557E-04 3.0036926E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 14:35:22 8.103u 0.234s 0:16.66 50.0% 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 Sat Oct 15 2011 at 14:35:22 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.793471 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 2.793471 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.485975 assigned positive charge : 434.1121 centred at (gu) : 86.06947 88.19122 86.44570 assigned negative charge : -436.5992 centred at (gu) : 85.73398 87.88661 86.34851 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 188380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26454 grid for indexing accessible points = 1.400000 m= 91275 mr = 134709 m= 30555 mr = 73243 m= 6361 mr = 23669 m= 691 mr = 4406 m= 39 mr = 402 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 5359 time to turn everything in is 1.000000 number of dielectric boundary points 80860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21806 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) : 1.862314 object centre at (A) : 20.01500 15.33600 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1709943 -0.2183015 midg,1,midg; midg,igrid,midg -0.2234018 -1.5821511E-02 1,midg,midg; igrid,midg,midg -0.6003601 0.3817489 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.240000 now iterating at: 14:35:23 rms-change max change #iterations 10.51546 280.2105 at 10iterations 6.247354 227.6022 at 20iterations 3.665471 88.89207 at 30iterations 2.149097 49.26448 at 40iterations 1.250519 25.97232 at 50iterations 0.7275596 13.91030 at 60iterations 0.4218072 7.994428 at 70iterations 0.2456754 4.682498 at 80iterations 0.1419522 2.770145 at 90iterations 8.2315221E-02 1.499271 at 100iterations 4.7548547E-02 0.8554993 at 110iterations 2.7517946E-02 0.5060301 at 120iterations 1.5878262E-02 0.2920380 at 130iterations 9.1628060E-03 0.1726475 at 140iterations 5.2896738E-03 9.6525073E-02 at 150iterations 3.0572419E-03 5.1292419E-02 at 160iterations 1.7637254E-03 2.9026031E-02 at 170iterations 1.0212767E-03 1.8206835E-02 at 180iterations finished qdiffx linear iterations at : 14:35:48 total time elapsed so far: 13.45000 # loops : 180 mean,max change (kT/e) : 1.0212767E-03 1.8206835E-02 energy calculations done at 13.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 14:35:48 13.592u 0.226s 0:26.72 51.6% 0+0k 0+0io 0pf+0w