Tue Oct 11 03:15:59 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 Tue Oct 11 2011 at 03:16:00 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5407 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.3427460 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): -25.01600 54.67900 ymin,ymax (A): -21.84600 73.04600 zmin,zma (A): -18.31400 85.55300 x,y,z range (A): 79.69500 94.89200 103.8670 scale (grids/A): 0.3427460 object centre (A): 14.83150 25.60000 33.61950 number of atom coordinates read : 5407 total number of charged atoms : 5002 net assigned charge : 1.500016 assigned positive charge : 792.9346 centred at (gu) : 90.83324 85.77003 96.44042 assigned negative charge : -791.4412 centred at (gu) : 90.82851 85.77646 96.43774 start vw surface at 0.2600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 3490 nv = 96 ne = 84 npr = 106779 no. pairs analyzed = 106779 no. exposed pairs = 6853 no. arc points = 48610 no. surface atoms = 2311 nbur = 3096 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.504320 m= 72 mr = 1501 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 2061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2628 ## 828 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 4626 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1494326E-17 5.2293218E-15 midg,1,midg; midg,igrid,midg 3.2995601E-15 -1.9952066E-17 1,midg,midg; igrid,midg,midg -7.9645764E-18 7.3464835E-16 gauss-seidel spectral radius is 0.9570991 estimated iterations to convergence 41 setup time was (sec) 0.7200000 now iterating at: 03:16:01 rms-change max change #iterations 8.4494054E-03 2.308374 at 10iterations 3.2215953E-04 0.1018906 at 20iterations 5.5392742E-05 1.9966125E-02 at 30iterations 1.0115717E-05 3.8356781E-03 at 40iterations 1.8575437E-06 7.2479248E-04 at 50iterations finished qdiffx linear iterations at : 03:16:03 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8575437E-06 7.2479248E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 03:16:04 3.559u 0.163s 0:04.15 89.3% 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 Tue Oct 11 2011 at 03:16:04 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5407 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.028238 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): -25.01600 54.67900 ymin,ymax (A): -21.84600 73.04600 zmin,zma (A): -18.31400 85.55300 x,y,z range (A): 79.69500 94.89200 103.8670 scale (grids/A): 1.028238 object centre (A): 14.83150 25.60000 33.61950 number of atom coordinates read : 5407 total number of charged atoms : 5002 net assigned charge : 1.500016 assigned positive charge : 792.9346 centred at (gu) : 92.49783 77.30814 109.3195 assigned negative charge : -791.4412 centred at (gu) : 92.48518 77.32890 109.3124 start vw surface at 0.2500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 43442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.268000 m= 6398 mr = 27123 m= 130 mr = 3035 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1384 time to turn everything in is 0.4600000 number of dielectric boundary points 19813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1164 ## 74 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 30025 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) : 0.3427460 object centre at (A) : 14.83150 25.60000 33.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9734738E-05 -9.2690880E-04 midg,1,midg; midg,igrid,midg 1.0189842E-03 3.4054214E-05 1,midg,midg; igrid,midg,midg -5.8219754E-05 2.2504621E-04 gauss-seidel spectral radius is 0.9953664 estimated iterations to convergence 118 setup time was (sec) 0.7200000 now iterating at: 03:16:05 rms-change max change #iterations 1.350309 91.31382 at 10iterations 0.3338608 19.21406 at 20iterations 8.3073072E-02 4.754776 at 30iterations 2.0809384E-02 1.168633 at 40iterations 5.1995553E-03 0.2926865 at 50iterations 1.3710542E-03 7.5920105E-02 at 60iterations 4.2944989E-04 2.6266098E-02 at 70iterations 1.7756224E-04 1.0808945E-02 at 80iterations 8.8627035E-05 5.7716370E-03 at 90iterations 4.7683257E-05 3.1776428E-03 at 100iterations 2.5968837E-05 1.7452240E-03 at 110iterations 1.4197737E-05 9.6321106E-04 at 120iterations finished qdiffx linear iterations at : 03:16:11 total time elapsed so far: 6.570000 # loops : 120 mean,max change (kT/e) : 1.4197737E-05 9.6321106E-04 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 03:16:11 6.750u 0.180s 0:07.34 94.4% 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 03:16:11 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5407 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.542357 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): -25.01600 54.67900 ymin,ymax (A): -21.84600 73.04600 zmin,zma (A): -18.31400 85.55300 x,y,z range (A): 79.69500 94.89200 103.8670 scale (grids/A): 1.542357 object centre (A): 14.83150 25.60000 33.61950 number of atom coordinates read : 5407 total number of charged atoms : 5002 net assigned charge : 1.500016 assigned positive charge : 792.9346 centred at (gu) : 93.74590 70.96179 118.9790 assigned negative charge : -791.4412 centred at (gu) : 93.72765 70.99313 118.9684 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 103515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.240000 m= 29021 mr = 69484 m= 2431 mr = 19686 m= 52 mr = 981 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 4664 time to turn everything in is 0.8300000 number of dielectric boundary points 44868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 463 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 37758 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) : 1.028238 object centre at (A) : 14.83150 25.60000 33.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5258431E-03 -0.1808119 midg,1,midg; midg,igrid,midg 4.9608126E-02 1.5841295E-03 1,midg,midg; igrid,midg,midg -2.4415150E-03 9.2906160E-03 gauss-seidel spectral radius is 0.9980246 estimated iterations to convergence 179 setup time was (sec) 1.140000 now iterating at: 03:16:13 rms-change max change #iterations 4.689605 200.2640 at 10iterations 1.948418 82.13050 at 20iterations 0.8012156 31.46889 at 30iterations 0.3281688 11.98498 at 40iterations 0.1340383 4.300420 at 50iterations 5.4560483E-02 2.077469 at 60iterations 2.2192050E-02 0.8673887 at 70iterations 9.0376260E-03 0.2791001 at 80iterations 3.6833824E-03 0.1230087 at 90iterations 1.5082265E-03 4.4322968E-02 at 100iterations 6.2863121E-04 1.9151688E-02 at 110iterations 2.7188440E-04 9.6130371E-03 at 120iterations 1.2611858E-04 5.4464340E-03 at 130iterations 6.5509310E-05 2.8953552E-03 at 140iterations 3.7945210E-05 1.7824173E-03 at 150iterations 2.3643470E-05 1.1386871E-03 at 160iterations 1.5330328E-05 7.4577332E-04 at 170iterations 1.0099463E-05 4.8637390E-04 at 180iterations finished qdiffx linear iterations at : 03:16:23 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 1.0099463E-05 4.8637390E-04 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 03:16:24 11.667u 0.254s 0:12.29 96.9% 0+0k 0+0io 0pf+0w