Sun Oct 9 08:10:59 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 08:10:59 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 = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 0.5592911 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 0.5592911 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 463.2473 centred at (gu) : 90.86108 89.70028 89.17547 assigned negative charge : -454.9273 centred at (gu) : 90.85859 89.59566 89.21135 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6379 nv = 96 ne = 84 npr = 62538 no. pairs analyzed = 62538 no. exposed pairs = 3845 no. arc points = 27614 no. surface atoms = 1284 nbur = 1810 mkacc time = 0.1700000 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 = 1.512000 m= 279 mr = 3333 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3800000 number of dielectric boundary points 3316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5303329E-09 3.8545075E-10 midg,1,midg; midg,igrid,midg -3.3611627E-10 1.8628217E-09 1,midg,midg; igrid,midg,midg 6.8233164E-10 1.0895003E-09 gauss-seidel spectral radius is 0.9835207 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 08:11:00 rms-change max change #iterations 8.7067708E-02 13.86274 at 10iterations 6.2835026E-03 1.037067 at 20iterations 5.3933467E-04 8.6841583E-02 at 30iterations 9.4406649E-05 1.2660980E-02 at 40iterations 2.4787150E-05 3.4199357E-03 at 50iterations finished qdiffx linear iterations at : 08:11:03 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.4787150E-05 3.4199357E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 08:11:04 4.109u 0.264s 0:04.64 93.9% 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 08:11:04 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 = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 1.677873 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 1.677873 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 463.2473 centred at (gu) : 92.58278 89.10032 87.52612 assigned negative charge : -454.9273 centred at (gu) : 92.57558 88.78690 87.63386 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27614 grid for indexing accessible points = 1.400000 m= 22042 mr = 47598 m= 2443 mr = 15006 m= 69 mr = 1152 m= 0 mr = 7 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 550 time to turn everything in is 0.6200000 number of dielectric boundary points 30752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22776 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) : 0.5592911 object centre at (A) : 30.73350 0.9339991 151.1200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3844067E-03 2.0802997E-03 midg,1,midg; midg,igrid,midg 1.1992891E-02 2.6527211E-02 1,midg,midg; igrid,midg,midg 4.9659060E-03 1.0501644E-02 gauss-seidel spectral radius is 0.9983045 estimated iterations to convergence 193 setup time was (sec) 0.9200000 now iterating at: 08:11:05 rms-change max change #iterations 3.625050 156.5397 at 10iterations 1.550270 56.01998 at 20iterations 0.6664582 22.15232 at 30iterations 0.2863643 10.20733 at 40iterations 0.1232768 4.108637 at 50iterations 5.2846279E-02 1.824336 at 60iterations 2.2667998E-02 0.8087921 at 70iterations 9.7901663E-03 0.3389449 at 80iterations 4.2141220E-03 0.1430988 at 90iterations 1.8214412E-03 6.8721771E-02 at 100iterations 7.9289143E-04 2.5897980E-02 at 110iterations 3.4642353E-04 1.1100769E-02 at 120iterations finished qdiffx linear iterations at : 08:11:13 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 3.4642353E-04 1.1100769E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 08:11:14 9.339u 0.292s 0:09.91 97.0% 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 Sun Oct 9 2011 at 08:11:14 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 = 3094 !!! WARNING: NDP 1031 has a net charge of -2.1790 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: 2.516810 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): 6.630000 54.83700 ymin,ymax (A): -30.89200 32.76000 zmin,zma (A): 124.6320 177.6080 x,y,z range (A): 48.20700 63.65200 52.97599 scale (grids/A): 2.516810 object centre (A): 30.73350 0.9339991 151.1200 number of atom coordinates read : 3094 total number of charged atoms : 2955 net assigned charge : 8.321023 assigned positive charge : 463.2473 centred at (gu) : 93.87377 88.65026 86.28888 assigned negative charge : -454.9273 centred at (gu) : 93.86327 88.18031 86.45067 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 162880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27614 grid for indexing accessible points = 1.400000 m= 74538 mr = 116782 m= 22316 mr = 58400 m= 3821 mr = 16793 m= 258 mr = 2393 m= 7 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 1955 time to turn everything in is 1.510000 number of dielectric boundary points 69344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 23619 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) : 1.677873 object centre at (A) : 30.73350 0.9339991 151.1200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6503287E-02 1.8693589E-02 midg,1,midg; midg,igrid,midg -2.3650577E-02 0.3596784 1,midg,midg; igrid,midg,midg 5.1943313E-02 0.1518375 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.830000 now iterating at: 08:11:16 rms-change max change #iterations 9.253474 305.8491 at 10iterations 5.289886 128.2220 at 20iterations 3.022940 71.09764 at 30iterations 1.713705 41.58889 at 40iterations 0.9674603 23.31592 at 50iterations 0.5450985 11.68600 at 60iterations 0.3071143 6.493446 at 70iterations 0.1722983 3.956633 at 80iterations 9.6891597E-02 2.549047 at 90iterations 5.4224364E-02 1.296627 at 100iterations 3.0362464E-02 0.7426987 at 110iterations 1.6982386E-02 0.3576813 at 120iterations 9.5046954E-03 0.1870394 at 130iterations 5.3166542E-03 0.1068177 at 140iterations 2.9699046E-03 6.2559128E-02 at 150iterations 1.6602934E-03 3.4908295E-02 at 160iterations 9.2678051E-04 1.9248962E-02 at 170iterations 5.1889644E-04 9.8075867E-03 at 180iterations finished qdiffx linear iterations at : 08:11:29 total time elapsed so far: 15.38000 # loops : 180 mean,max change (kT/e) : 5.1889644E-04 9.8075867E-03 energy calculations done at 15.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 08:11:30 15.561u 0.321s 0:16.14 98.3% 0+0k 0+0io 0pf+0w