Mon Oct 10 13:55:55 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 13:55:55 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 !!! WARNING: ASL 35 has a net charge of -0.1000 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: 0.7374570 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 0.7374570 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -4.099988 assigned positive charge : 313.4719 centred at (gu) : 90.93816 89.77209 90.06203 assigned negative charge : -317.5720 centred at (gu) : 90.86698 89.73450 90.21883 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7738 nv = 96 ne = 84 npr = 43327 no. pairs analyzed = 43327 no. exposed pairs = 2630 no. arc points = 18547 no. surface atoms = 881 nbur = 1202 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 542 mr = 4328 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 172 time to turn everything in is 0.2600000 number of dielectric boundary points 3846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1456 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8055301E-08 -2.2357689E-07 midg,1,midg; midg,igrid,midg -1.0930005E-07 -3.1638880E-08 1,midg,midg; igrid,midg,midg -1.1531306E-07 -3.7934980E-10 gauss-seidel spectral radius is 0.9904155 estimated iterations to convergence 83 setup time was (sec) 0.4800000 now iterating at: 13:55:56 rms-change max change #iterations 0.2452837 31.31425 at 10iterations 3.3297621E-02 4.718239 at 20iterations 4.4291737E-03 0.6224136 at 30iterations 5.9001381E-04 7.7503204E-02 at 40iterations 7.9319987E-05 9.9153519E-03 at 50iterations finished qdiffx linear iterations at : 13:55:59 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.9319987E-05 9.9153519E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 13:56:00 3.521u 0.225s 0:04.34 86.1% 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 13:56:00 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 !!! WARNING: ASL 35 has a net charge of -0.1000 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: 2.212371 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 2.212371 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -4.099988 assigned positive charge : 313.4719 centred at (gu) : 92.81439 89.31635 90.18609 assigned negative charge : -317.5720 centred at (gu) : 92.60081 89.20385 90.65660 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18547 grid for indexing accessible points = 1.400000 m= 32245 mr = 56214 m= 6964 mr = 24594 m= 763 mr = 4829 m= 32 mr = 407 m= 0 mr = 8 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4074 time to turn everything in is 0.5900000 number of dielectric boundary points 35287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15487 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) : 0.7374570 object centre at (A) : 1.498000 30.60650 44.91750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2921322E-03 -9.7716764E-02 midg,1,midg; midg,igrid,midg -2.5615001E-02 -1.8882945E-02 1,midg,midg; igrid,midg,midg -3.1762436E-02 2.1608662E-02 gauss-seidel spectral radius is 0.9989172 estimated iterations to convergence 240 setup time was (sec) 0.9200000 now iterating at: 13:56:01 rms-change max change #iterations 5.043986 205.2418 at 10iterations 2.553981 83.65153 at 20iterations 1.302274 37.02201 at 30iterations 0.6592886 21.68911 at 40iterations 0.3355815 9.628368 at 50iterations 0.1705036 5.005302 at 60iterations 8.6692519E-02 2.517226 at 70iterations 4.4032857E-02 1.180811 at 80iterations 2.2479830E-02 0.6295261 at 90iterations 1.1382031E-02 0.3292828 at 100iterations 5.8054612E-03 0.1747081 at 110iterations 2.9432965E-03 8.4239960E-02 at 120iterations finished qdiffx linear iterations at : 13:56:07 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.9432965E-03 8.4239960E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 13:56:08 7.626u 0.215s 0:08.40 93.2% 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 13:56:08 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2083 !!! WARNING: ASL 35 has a net charge of -0.1000 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: 3.318557 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): -22.63900 25.63500 ymin,ymax (A): 9.026000 52.18700 zmin,zma (A): 20.82100 69.01400 x,y,z range (A): 48.27400 43.16100 48.19300 scale (grids/A): 3.318557 object centre (A): 1.498000 30.60650 44.91750 number of atom coordinates read : 2083 total number of charged atoms : 1946 net assigned charge : -4.099988 assigned positive charge : 313.4719 centred at (gu) : 94.22158 88.97448 90.27894 assigned negative charge : -317.5720 centred at (gu) : 93.90118 88.80575 90.98492 start vw surface at 0.1600000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 187360 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18547 grid for indexing accessible points = 1.400000 m= 99343 mr = 135533 m= 42143 mr = 82413 m= 13382 mr = 34980 m= 3089 mr = 10610 m= 421 mr = 2362 m= 32 mr = 268 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 14152 time to turn everything in is 1.960000 number of dielectric boundary points 79585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 15568 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) : 2.212371 object centre at (A) : 1.498000 30.60650 44.91750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6940870E-03 -0.9671717 midg,1,midg; midg,igrid,midg -0.1103393 -0.1970294 1,midg,midg; igrid,midg,midg -0.3850985 0.1644934 gauss-seidel spectral radius is 0.9993155 estimated iterations to convergence 302 setup time was (sec) 2.270000 now iterating at: 13:56:11 rms-change max change #iterations 10.92655 323.2933 at 10iterations 6.412014 130.8367 at 20iterations 3.776623 85.31279 at 30iterations 2.218506 41.81039 at 40iterations 1.303500 21.41106 at 50iterations 0.7654344 12.85980 at 60iterations 0.4487918 7.528156 at 70iterations 0.2633929 4.142126 at 80iterations 0.1548599 2.839298 at 90iterations 9.0521082E-02 1.543172 at 100iterations 5.3217527E-02 0.8691368 at 110iterations 3.1139238E-02 0.5230312 at 120iterations 1.8308949E-02 0.3273611 at 130iterations 1.0733653E-02 0.1743659 at 140iterations 6.2793349E-03 0.1218872 at 150iterations 3.6937892E-03 6.2604904E-02 at 160iterations 2.1591536E-03 3.7873268E-02 at 170iterations 1.2690745E-03 2.3277283E-02 at 180iterations finished qdiffx linear iterations at : 13:56:21 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 1.2690745E-03 2.3277283E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 13:56:22 12.981u 0.216s 0:13.60 96.9% 0+0k 0+0io 0pf+0w