Tue Oct 11 03:48:57 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 Tue Oct 11 2011 at 03:48:57 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 = 2895 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6607029 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 0.6607029 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 441.4136 centred at (gu) : 89.93290 90.35551 88.96661 assigned negative charge : -439.7132 centred at (gu) : 90.18720 90.24138 88.96989 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8392 nv = 96 ne = 84 npr = 59499 no. pairs analyzed = 59499 no. exposed pairs = 3488 no. arc points = 24221 no. surface atoms = 1173 nbur = 1722 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 461 mr = 4822 m= 0 mr = 69 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2200000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2360 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 10044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2816867E-09 2.9367668E-09 midg,1,midg; midg,igrid,midg -2.0391447E-08 3.2405342E-08 1,midg,midg; igrid,midg,midg 6.1679799E-08 -5.4467868E-08 gauss-seidel spectral radius is 0.9881486 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 03:48:57 rms-change max change #iterations 0.1776192 23.04316 at 10iterations 1.9797014E-02 2.308212 at 20iterations 2.2369099E-03 0.2685795 at 30iterations 3.2543449E-04 4.2154312E-02 at 40iterations 7.9436330E-05 9.0065002E-03 at 50iterations finished qdiffx linear iterations at : 03:49:00 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.9436330E-05 9.0065002E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:49:01 3.396u 0.182s 0:04.00 89.2% 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 Tue Oct 11 2011 at 03:49:01 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 = 2895 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.982109 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 1.982109 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 441.4136 centred at (gu) : 89.79824 91.06633 86.89945 assigned negative charge : -439.7132 centred at (gu) : 90.56152 90.72377 86.90958 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 34779 mr = 64734 m= 5811 mr = 26367 m= 431 mr = 3819 m= 11 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1194 time to turn everything in is 0.4300000 number of dielectric boundary points 36635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 21617 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) : 0.6607029 object centre at (A) : 9.570002 31.21550 52.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9756118E-03 -2.1909343E-02 midg,1,midg; midg,igrid,midg -1.3680470E-02 1.7856985E-02 1,midg,midg; igrid,midg,midg 8.0969639E-02 -1.2362302E-02 gauss-seidel spectral radius is 0.9987622 estimated iterations to convergence 225 setup time was (sec) 0.6400000 now iterating at: 03:49:02 rms-change max change #iterations 4.990219 231.8201 at 10iterations 2.435129 79.20600 at 20iterations 1.180010 33.62556 at 30iterations 0.5756115 17.16086 at 40iterations 0.2804669 9.559351 at 50iterations 0.1359253 3.859885 at 60iterations 6.6392615E-02 2.029137 at 70iterations 3.2302160E-02 0.8911018 at 80iterations 1.5716944E-02 0.4274020 at 90iterations 7.7014626E-03 0.2206345 at 100iterations 3.7684888E-03 0.1067038 at 110iterations 1.8688411E-03 5.6016922E-02 at 120iterations finished qdiffx linear iterations at : 03:49:09 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.8688411E-03 5.6016922E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 03:49:10 7.895u 0.231s 0:08.97 90.5% 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 Tue Oct 11 2011 at 03:49:10 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.973163 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): -15.41300 34.55300 ymin,ymax (A): 7.001000 55.43000 zmin,zma (A): 25.97200 79.85400 x,y,z range (A): 49.96600 48.42900 53.88200 scale (grids/A): 2.973163 object centre (A): 9.570002 31.21550 52.91300 number of atom coordinates read : 2895 total number of charged atoms : 2739 net assigned charge : 1.701019 assigned positive charge : 441.4136 centred at (gu) : 89.69707 91.59945 85.34903 assigned negative charge : -439.7132 centred at (gu) : 90.84215 91.08569 85.36429 start vw surface at 0.1000000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 209413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 111502 mr = 155877 m= 41915 mr = 93045 m= 10723 mr = 34279 m= 1806 mr = 8302 m= 138 mr = 1318 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 3945 time to turn everything in is 1.180000 number of dielectric boundary points 82617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 21908 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) : 1.982109 object centre at (A) : 9.570002 31.21550 52.91300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1044556 -0.2974617 midg,1,midg; midg,igrid,midg -0.1546636 0.2245281 1,midg,midg; igrid,midg,midg 0.6908128 -7.8162894E-02 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 03:49:12 rms-change max change #iterations 11.34429 505.0035 at 10iterations 6.688544 147.3006 at 20iterations 3.943933 78.73564 at 30iterations 2.311973 44.01211 at 40iterations 1.357691 26.22346 at 50iterations 0.7961476 15.62397 at 60iterations 0.4663355 8.666121 at 70iterations 0.2726310 5.181137 at 80iterations 0.1593110 2.733714 at 90iterations 9.3024418E-02 1.519692 at 100iterations 5.4221440E-02 0.8814640 at 110iterations 3.1759810E-02 0.5493259 at 120iterations 1.8519707E-02 0.3176384 at 130iterations 1.0821266E-02 0.1758327 at 140iterations 6.3368320E-03 0.1039715 at 150iterations 3.7172884E-03 5.9062958E-02 at 160iterations 2.1923971E-03 3.8429260E-02 at 170iterations 1.3028804E-03 2.1591187E-02 at 180iterations finished qdiffx linear iterations at : 03:49:23 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 1.3028804E-03 2.1591187E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 03:49:24 13.093u 0.227s 0:13.71 97.0% 0+0k 0+0io 0pf+0w