Sat Oct 8 22:55:20 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 8 2011 at 22:55:20 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.6026238 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 0.6026238 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 375.8159 centred at (gu) : 90.78341 89.76995 91.90689 assigned negative charge : -370.5909 centred at (gu) : 90.68694 89.89516 92.01912 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 52331 no. pairs analyzed = 52331 no. exposed pairs = 3235 no. arc points = 22957 no. surface atoms = 1099 nbur = 1486 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3442 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2393 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7928 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3404458E-09 -2.8860168E-09 midg,1,midg; midg,igrid,midg 7.5006934E-09 -2.1704334E-09 1,midg,midg; igrid,midg,midg -9.7291730E-10 7.2456157E-09 gauss-seidel spectral radius is 0.9857510 estimated iterations to convergence 69 setup time was (sec) 0.5400000 now iterating at: 22:55:21 rms-change max change #iterations 0.1108941 16.51338 at 10iterations 9.5674107E-03 1.550335 at 20iterations 8.1225432E-04 0.1126862 at 30iterations 6.9491289E-05 1.2081146E-02 at 40iterations 5.9687950E-06 9.9599361E-04 at 50iterations finished qdiffx linear iterations at : 22:55:23 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 5.9687950E-06 9.9599361E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 22:55:24 3.291u 0.171s 0:03.74 92.5% 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 8 2011 at 22:55:24 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.807871 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 1.807871 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 375.8159 centred at (gu) : 92.34979 89.30914 95.72002 assigned negative charge : -370.5909 centred at (gu) : 92.06065 89.68537 96.05716 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69621 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22957 grid for indexing accessible points = 1.400000 m= 23956 mr = 47827 m= 3378 mr = 17179 m= 142 mr = 1920 m= 0 mr = 33 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.4900000 number of dielectric boundary points 30138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19149 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) : 0.6026238 object centre at (A) : 8.157499 47.43650 56.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7464116E-02 4.6219388E-03 midg,1,midg; midg,igrid,midg 5.6904465E-02 4.9684010E-04 1,midg,midg; igrid,midg,midg -5.9032147E-03 5.8954488E-03 gauss-seidel spectral radius is 0.9984872 estimated iterations to convergence 204 setup time was (sec) 0.7800000 now iterating at: 22:55:25 rms-change max change #iterations 3.747429 168.2062 at 10iterations 1.682436 65.88049 at 20iterations 0.7577311 26.27512 at 30iterations 0.3397559 11.77797 at 40iterations 0.1531228 5.246357 at 50iterations 6.8558559E-02 2.266141 at 60iterations 3.0912869E-02 1.133919 at 70iterations 1.3885600E-02 0.5557203 at 80iterations 6.2505016E-03 0.2061768 at 90iterations 2.7976227E-03 9.1838837E-02 at 100iterations 1.2644007E-03 4.4494629E-02 at 110iterations 5.6860934E-04 1.8155932E-02 at 120iterations finished qdiffx linear iterations at : 22:55:31 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 5.6860934E-04 1.8155932E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 22:55:31 7.330u 0.211s 0:07.85 96.0% 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 8 2011 at 22:55:32 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.711807 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): -15.68500 32.00000 ymin,ymax (A): 17.89900 76.97400 zmin,zma (A): 30.81000 81.36000 x,y,z range (A): 47.68500 59.07500 50.55000 scale (grids/A): 2.711807 object centre (A): 8.157499 47.43650 56.08500 number of atom coordinates read : 2585 total number of charged atoms : 2445 net assigned charge : 5.226027 assigned positive charge : 375.8159 centred at (gu) : 93.52442 88.96363 98.57975 assigned negative charge : -370.5909 centred at (gu) : 93.09110 89.52798 99.08572 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 161079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22957 grid for indexing accessible points = 1.400000 m= 79088 mr = 116357 m= 27091 mr = 63776 m= 5818 mr = 21140 m= 698 mr = 4158 m= 25 mr = 428 m= 0 mr = 5 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 3618 time to turn everything in is 1.210000 number of dielectric boundary points 67935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 19537 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) : 1.807871 object centre at (A) : 8.157499 47.43650 56.08500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3956556 5.5111885E-02 midg,1,midg; midg,igrid,midg 0.8229392 8.3309330E-02 1,midg,midg; igrid,midg,midg -3.8887568E-02 7.1262918E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 1.530000 now iterating at: 22:55:33 rms-change max change #iterations 9.126957 282.6658 at 10iterations 5.246124 136.7105 at 20iterations 3.005815 71.84296 at 30iterations 1.715111 33.26862 at 40iterations 0.9739829 17.60818 at 50iterations 0.5517628 10.60273 at 60iterations 0.3132348 6.167711 at 70iterations 0.1772827 3.470558 at 80iterations 0.1003527 2.238312 at 90iterations 5.6775760E-02 1.194494 at 100iterations 3.2115888E-02 0.6056194 at 110iterations 1.8139711E-02 0.3642826 at 120iterations 1.0260550E-02 0.1944389 at 130iterations 5.8009266E-03 0.1133795 at 140iterations 3.2788797E-03 6.4588070E-02 at 150iterations 1.8532810E-03 3.4065247E-02 at 160iterations 1.0480023E-03 1.9630432E-02 at 170iterations 5.9262133E-04 1.1299133E-02 at 180iterations finished qdiffx linear iterations at : 22:55:45 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 5.9262133E-04 1.1299133E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 22:55:45 13.259u 0.202s 0:13.73 97.9% 0+0k 0+0io 0pf+0w