Sat Oct 15 11:03:00 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 15 2011 at 11:03:01 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4383 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5587031 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66500 zmin,zma (A): 31.13200 89.11100 x,y,z range (A): 60.22600 63.71900 57.97900 scale (grids/A): 0.5587031 object centre (A): 4.992000 66.80550 60.12150 number of atom coordinates read : 4383 total number of charged atoms : 4234 net assigned charge : -1.985943 assigned positive charge : 662.5493 centred at (gu) : 90.78047 88.35264 88.93726 assigned negative charge : -664.5383 centred at (gu) : 90.62596 88.48582 89.08602 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8741 nv = 96 ne = 84 npr = 92320 no. pairs analyzed = 92320 no. exposed pairs = 4869 no. arc points = 33402 no. surface atoms = 1651 nbur = 2732 mkacc time = 0.2400000 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 = 1.540000 m= 356 mr = 5091 m= 0 mr = 37 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.5000000 number of dielectric boundary points 3969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3438 ## 419 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11588 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6300311E-09 -2.0594930E-09 midg,1,midg; midg,igrid,midg 2.6899767E-09 -1.6180056E-09 1,midg,midg; igrid,midg,midg -2.2834963E-09 2.5564932E-09 gauss-seidel spectral radius is 0.9835724 estimated iterations to convergence 64 setup time was (sec) 0.8100000 now iterating at: 11:03:02 rms-change max change #iterations 0.1010188 14.68432 at 10iterations 7.4357325E-03 1.009678 at 20iterations 7.0014974E-04 8.6019516E-02 at 30iterations 1.4949979E-04 1.9732952E-02 at 40iterations 4.7163983E-05 6.5593719E-03 at 50iterations finished qdiffx linear iterations at : 11:03:06 total time elapsed so far: 5.570000 # loops : 50 mean,max change (kT/e) : 4.7163983E-05 6.5593719E-03 energy calculations done at 5.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.740000 DelPhi exited at 11:03:07 5.744u 0.426s 0:06.67 92.3% 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 15 2011 at 11:03:07 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4383 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.676109 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66500 zmin,zma (A): 31.13200 89.11100 x,y,z range (A): 60.22600 63.71900 57.97900 scale (grids/A): 1.676109 object centre (A): 4.992000 66.80550 60.12150 number of atom coordinates read : 4383 total number of charged atoms : 4234 net assigned charge : -1.985943 assigned positive charge : 662.5493 centred at (gu) : 92.34019 85.05675 86.81050 assigned negative charge : -664.5383 centred at (gu) : 91.87755 85.45721 87.25750 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98221 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33402 grid for indexing accessible points = 1.400000 m= 31636 mr = 71492 m= 3673 mr = 23100 m= 105 mr = 2209 m= 0 mr = 24 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 7353 time to turn everything in is 0.8100000 number of dielectric boundary points 36810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 368 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 32615 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) : 0.5587031 object centre at (A) : 4.992000 66.80550 60.12150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0507496E-02 -2.2700403E-02 midg,1,midg; midg,igrid,midg 2.9333489E-02 -7.3177256E-03 1,midg,midg; igrid,midg,midg -1.8904349E-02 3.1842329E-02 gauss-seidel spectral radius is 0.9984044 estimated iterations to convergence 199 setup time was (sec) 1.240000 now iterating at: 11:03:09 rms-change max change #iterations 4.410297 184.2359 at 10iterations 1.943644 60.56768 at 20iterations 0.8604670 26.72719 at 30iterations 0.3802927 11.36603 at 40iterations 0.1675008 5.533749 at 50iterations 7.3809825E-02 2.180897 at 60iterations 3.2572813E-02 0.9476509 at 70iterations 1.4475455E-02 0.4192824 at 80iterations 6.4272308E-03 0.1876678 at 90iterations 2.8594972E-03 8.1056595E-02 at 100iterations 1.2927179E-03 3.7738323E-02 at 110iterations 6.0118077E-04 1.8898010E-02 at 120iterations finished qdiffx linear iterations at : 11:03:22 total time elapsed so far: 14.18000 # loops : 120 mean,max change (kT/e) : 6.0118077E-04 1.8898010E-02 energy calculations done at 14.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.35000 DelPhi exited at 11:03:22 14.357u 0.498s 0:15.16 97.8% 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 Sat Oct 15 2011 at 11:03:22 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4383 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.514164 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66500 zmin,zma (A): 31.13200 89.11100 x,y,z range (A): 60.22600 63.71900 57.97900 scale (grids/A): 2.514164 object centre (A): 4.992000 66.80550 60.12150 number of atom coordinates read : 4383 total number of charged atoms : 4234 net assigned charge : -1.985943 assigned positive charge : 662.5493 centred at (gu) : 93.50999 82.58476 85.21549 assigned negative charge : -664.5383 centred at (gu) : 92.81618 83.18568 85.88616 start vw surface at 0.1700000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 228717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33402 grid for indexing accessible points = 1.400000 m= 109585 mr = 173691 m= 32426 mr = 90108 m= 6166 mr = 25647 m= 580 mr = 4593 m= 17 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 24729 time to turn everything in is 2.170000 number of dielectric boundary points 83105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 33853 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) : 1.676109 object centre at (A) : 4.992000 66.80550 60.12150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6014320 -0.2938541 midg,1,midg; midg,igrid,midg 0.4388125 -8.6731196E-04 1,midg,midg; igrid,midg,midg -0.2591449 0.3570746 gauss-seidel spectral radius is 0.9992216 estimated iterations to convergence 283 setup time was (sec) 2.600000 now iterating at: 11:03:26 rms-change max change #iterations 11.07247 326.2451 at 10iterations 6.380000 134.6619 at 20iterations 3.666621 67.10677 at 30iterations 2.093210 38.95424 at 40iterations 1.194603 22.95040 at 50iterations 0.6803815 12.25508 at 60iterations 0.3881712 7.448195 at 70iterations 0.2207506 3.669039 at 80iterations 0.1251769 2.021624 at 90iterations 7.1082875E-02 1.134159 at 100iterations 4.0435866E-02 0.6579094 at 110iterations 2.2944879E-02 0.4020240 at 120iterations 1.3028503E-02 0.2162094 at 130iterations 7.4066226E-03 0.1304760 at 140iterations 4.2143795E-03 7.2578430E-02 at 150iterations 2.4111518E-03 3.8710594E-02 at 160iterations 1.3854475E-03 2.2537231E-02 at 170iterations 8.0767623E-04 1.4100075E-02 at 180iterations finished qdiffx linear iterations at : 11:03:47 total time elapsed so far: 24.35000 # loops : 180 mean,max change (kT/e) : 8.0767623E-04 1.4100075E-02 energy calculations done at 24.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.53000 DelPhi exited at 11:03:48 24.531u 0.516s 0:25.64 97.6% 0+0k 0+0io 0pf+0w