Mon Oct 10 17:04:10 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 17:04:10 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIR 77 has a net charge of 0.5140 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: GLM 281 has a net charge of -0.0940 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 0.5876527 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 0.5876527 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3291 net assigned charge : 6.120036 assigned positive charge : 526.2060 centred at (gu) : 88.72572 88.90400 90.64761 assigned negative charge : -520.0879 centred at (gu) : 88.75012 89.02751 90.50128 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7696 nv = 96 ne = 84 npr = 70163 no. pairs analyzed = 70163 no. exposed pairs = 4496 no. arc points = 31219 no. surface atoms = 1475 nbur = 1968 mkacc time = 0.1200000 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 = 1.456000 m= 399 mr = 3990 m= 0 mr = 36 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3087 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7969007E-09 7.4312747E-09 midg,1,midg; midg,igrid,midg 7.3106858E-09 -1.9106750E-09 1,midg,midg; igrid,midg,midg 3.2752241E-09 6.3936162E-10 gauss-seidel spectral radius is 0.9850890 estimated iterations to convergence 67 setup time was (sec) 0.4400000 now iterating at: 17:04:11 rms-change max change #iterations 0.1166045 16.74956 at 10iterations 9.7406330E-03 1.300156 at 20iterations 1.1329318E-03 0.1492043 at 30iterations 2.7416283E-04 3.8636208E-02 at 40iterations 8.7049957E-05 1.2227058E-02 at 50iterations finished qdiffx linear iterations at : 17:04:14 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 8.7049957E-05 1.2227058E-02 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 17:04:15 3.685u 0.223s 0:04.94 78.9% 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 Mon Oct 10 2011 at 17:04:15 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIR 77 has a net charge of 0.5140 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: GLM 281 has a net charge of -0.0940 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 1.762958 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 1.762958 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3291 net assigned charge : 6.120036 assigned positive charge : 526.2060 centred at (gu) : 86.17630 86.71118 91.94188 assigned negative charge : -520.0879 centred at (gu) : 86.24997 87.08219 91.50340 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 84271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31219 grid for indexing accessible points = 1.400000 m= 28845 mr = 57215 m= 4003 mr = 19993 m= 155 mr = 2176 m= 0 mr = 39 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 0.4400000 number of dielectric boundary points 37851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 25628 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) : 0.5876527 object centre at (A) : -21.53150 7.728998 -37.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7592700E-02 3.1995490E-02 midg,1,midg; midg,igrid,midg 3.2894623E-02 -1.5577334E-02 1,midg,midg; igrid,midg,midg 2.3223417E-02 2.7596918E-03 gauss-seidel spectral radius is 0.9985014 estimated iterations to convergence 205 setup time was (sec) 0.6800000 now iterating at: 17:04:16 rms-change max change #iterations 4.320848 179.1394 at 10iterations 1.944692 71.33394 at 20iterations 0.8812057 27.72761 at 30iterations 0.3961167 12.16662 at 40iterations 0.1793265 5.584923 at 50iterations 8.0974989E-02 2.489113 at 60iterations 3.6770757E-02 1.078032 at 70iterations 1.6685821E-02 0.5472593 at 80iterations 7.6012756E-03 0.2372389 at 90iterations 3.4890322E-03 0.1109142 at 100iterations 1.6341950E-03 5.3840637E-02 at 110iterations 7.8765303E-04 2.5892258E-02 at 120iterations finished qdiffx linear iterations at : 17:04:23 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 7.8765303E-04 2.5892258E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 17:04:24 8.476u 0.244s 0:09.45 92.1% 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 17:04:24 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3443 !!! WARNING: HIR 77 has a net charge of 0.5140 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: GLM 281 has a net charge of -0.0940 !!! WARNING: MG6 686 has a net charge of 1.4000 !!! WARNING: ZN6 688 has a net charge of 1.4000 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: 2.644437 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): -50.23100 7.168000 ymin,ymax (A): -22.56100 38.01900 zmin,zma (A): -64.76900 -9.707999 x,y,z range (A): 57.39900 60.58000 55.06100 scale (grids/A): 2.644437 object centre (A): -21.53150 7.728998 -37.23850 number of atom coordinates read : 3443 total number of charged atoms : 3291 net assigned charge : 6.120036 assigned positive charge : 526.2060 centred at (gu) : 84.26406 85.06623 92.91248 assigned negative charge : -520.0879 centred at (gu) : 84.37497 85.62336 92.25501 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31219 grid for indexing accessible points = 1.400000 m= 94373 mr = 139833 m= 32306 mr = 74429 m= 6753 mr = 24717 m= 710 mr = 4696 m= 27 mr = 399 m= 0 mr = 8 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 758 time to turn everything in is 1.050000 number of dielectric boundary points 85399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 26322 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) : 1.762958 object centre at (A) : -21.53150 7.728998 -37.23850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2316635 0.3778718 midg,1,midg; midg,igrid,midg 0.4240946 -0.1360951 1,midg,midg; igrid,midg,midg 0.2301491 9.2214935E-02 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.310000 now iterating at: 17:04:26 rms-change max change #iterations 10.71009 286.1693 at 10iterations 6.289857 147.3174 at 20iterations 3.682819 91.80934 at 30iterations 2.140071 48.08372 at 40iterations 1.240146 28.70043 at 50iterations 0.7172883 16.46569 at 60iterations 0.4129051 8.390303 at 70iterations 0.2374822 4.630334 at 80iterations 0.1365051 2.952866 at 90iterations 7.8413278E-02 1.468939 at 100iterations 4.5015033E-02 0.8959885 at 110iterations 2.5827868E-02 0.5002670 at 120iterations 1.4774383E-02 0.2742682 at 130iterations 8.4849522E-03 0.1600103 at 140iterations 4.8690084E-03 9.4160080E-02 at 150iterations 2.8132610E-03 4.9280345E-02 at 160iterations 1.6321252E-03 2.8128624E-02 at 170iterations 9.5930335E-04 2.0141602E-02 at 180iterations finished qdiffx linear iterations at : 17:04:40 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 9.5930335E-04 2.0141602E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.14000 DelPhi exited at 17:04:40 15.140u 0.248s 0:15.82 97.2% 0+0k 0+0io 0pf+0w