Sun Oct 9 14:02:32 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+sph.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 = amb.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 14:02:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 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: 0.6810790 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 0.6810790 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 363.1660 centred at (gu) : 90.39178 89.05699 88.99446 assigned negative charge : -359.6666 centred at (gu) : 90.41595 88.91099 88.91467 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7446 nv = 96 ne = 84 npr = 47806 no. pairs analyzed = 47806 no. exposed pairs = 2857 no. arc points = 20434 no. surface atoms = 966 nbur = 1412 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4193 m= 0 mr = 52 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.1800000 number of dielectric boundary points 3650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1988 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8555 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0786257E-08 3.3268670E-08 midg,1,midg; midg,igrid,midg -3.6096871E-08 5.0148778E-08 1,midg,midg; igrid,midg,midg 2.1944958E-08 9.4629682E-09 gauss-seidel spectral radius is 0.9888017 estimated iterations to convergence 77 setup time was (sec) 0.3600000 now iterating at: 14:02:33 rms-change max change #iterations 0.1812765 27.65951 at 10iterations 2.0518983E-02 3.510059 at 20iterations 2.4688041E-03 0.4297676 at 30iterations 3.5463128E-04 6.3755035E-02 at 40iterations 7.5900927E-05 1.2214661E-02 at 50iterations finished qdiffx linear iterations at : 14:02:36 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 7.5900927E-05 1.2214661E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:02:36 3.399u 0.202s 0:03.91 91.8% 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 14:02:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 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: 2.043237 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 2.043237 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 363.1660 centred at (gu) : 91.17454 87.17066 86.98298 assigned negative charge : -359.6666 centred at (gu) : 91.24746 86.73283 86.74364 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 79596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20434 grid for indexing accessible points = 1.400000 m= 29814 mr = 55819 m= 5056 mr = 22369 m= 419 mr = 3128 m= 8 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2223 time to turn everything in is 0.3600000 number of dielectric boundary points 33381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17696 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) : 0.6810790 object centre at (A) : 45.99450 24.18200 15.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9962548E-03 4.0545836E-02 midg,1,midg; midg,igrid,midg -4.3621346E-02 1.3537582E-02 1,midg,midg; igrid,midg,midg 3.6009252E-02 -1.3703235E-02 gauss-seidel spectral radius is 0.9987852 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 14:02:37 rms-change max change #iterations 4.649115 221.7525 at 10iterations 2.265225 74.68092 at 20iterations 1.107866 36.10361 at 30iterations 0.5430617 15.93413 at 40iterations 0.2655743 7.691324 at 50iterations 0.1297635 3.676529 at 60iterations 6.3503265E-02 1.769209 at 70iterations 3.1070065E-02 0.9816365 at 80iterations 1.5306884E-02 0.4619842 at 90iterations 7.5035538E-03 0.2112522 at 100iterations 3.7027448E-03 0.1087322 at 110iterations 1.8472893E-03 5.5555344E-02 at 120iterations finished qdiffx linear iterations at : 14:02:44 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.8472893E-03 5.5555344E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 14:02:45 7.947u 0.225s 0:08.50 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 Sun Oct 9 2011 at 14:02:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2378 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: 3.064856 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): 21.50700 70.48200 ymin,ymax (A): -1.953000 50.31700 zmin,zma (A): -5.664000 37.46000 x,y,z range (A): 48.97500 52.27000 43.12400 scale (grids/A): 3.064856 object centre (A): 45.99450 24.18200 15.89800 number of atom coordinates read : 2378 total number of charged atoms : 2236 net assigned charge : 3.500023 assigned positive charge : 363.1660 centred at (gu) : 91.76165 85.75593 85.47431 assigned negative charge : -359.6666 centred at (gu) : 91.87112 85.09917 85.11535 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20434 grid for indexing accessible points = 1.400000 m= 95882 mr = 134722 m= 35828 mr = 79329 m= 9164 mr = 29108 m= 1630 mr = 6842 m= 164 mr = 1120 m= 4 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 7671 time to turn everything in is 1.030000 number of dielectric boundary points 75169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 17888 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) : 2.043237 object centre at (A) : 45.99450 24.18200 15.89800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2496838E-02 0.3790015 midg,1,midg; midg,igrid,midg -0.5562979 0.3300754 1,midg,midg; igrid,midg,midg 0.3747227 -0.3664672 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 14:02:46 rms-change max change #iterations 10.57143 409.2784 at 10iterations 6.224640 141.0481 at 20iterations 3.658577 72.92522 at 30iterations 2.144343 43.53477 at 40iterations 1.256873 23.48399 at 50iterations 0.7354661 13.99917 at 60iterations 0.4286946 7.536439 at 70iterations 0.2503423 4.710383 at 80iterations 0.1456980 2.823816 at 90iterations 8.4895946E-02 1.480802 at 100iterations 4.9420394E-02 0.8448105 at 110iterations 2.8755005E-02 0.5035858 at 120iterations 1.6750388E-02 0.2884645 at 130iterations 9.7854333E-03 0.1811552 at 140iterations 5.7113948E-03 0.1028595 at 150iterations 3.3551732E-03 5.4930568E-02 at 160iterations 1.9905285E-03 3.4473419E-02 at 170iterations 1.1986670E-03 2.1545410E-02 at 180iterations finished qdiffx linear iterations at : 14:02:58 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.1986670E-03 2.1545410E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 14:02:58 12.860u 0.208s 0:13.33 97.9% 0+0k 0+0io 0pf+0w