Mon Oct 10 16:04:25 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 16:04:26 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4166 !!! WARNING: ASP 607 has a net charge of -2.0000 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: 0.5352498 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): -19.67900 31.90700 ymin,ymax (A): -34.63100 29.63200 zmin,zma (A): -26.84700 39.66400 x,y,z range (A): 51.58600 64.26300 66.51100 scale (grids/A): 0.5352498 object centre (A): 6.114000 -2.499500 6.408499 number of atom coordinates read : 4166 total number of charged atoms : 4018 net assigned charge : 3.500010 assigned positive charge : 614.5282 centred at (gu) : 90.81980 90.21394 87.60925 assigned negative charge : -611.0309 centred at (gu) : 90.85163 90.25767 87.62480 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7750 nv = 96 ne = 84 npr = 84642 no. pairs analyzed = 84642 no. exposed pairs = 5046 no. arc points = 34858 no. surface atoms = 1702 nbur = 2464 mkacc time = 0.1500000 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 = 1.596000 m= 289 mr = 4233 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2800000 number of dielectric boundary points 3794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3463 ## 466 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10238 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2878684E-10 2.7802231E-11 midg,1,midg; midg,igrid,midg 3.8123926E-10 -1.3114124E-10 1,midg,midg; igrid,midg,midg 2.7003069E-10 -6.5329187E-11 gauss-seidel spectral radius is 0.9820986 estimated iterations to convergence 62 setup time was (sec) 0.4700000 now iterating at: 16:04:26 rms-change max change #iterations 8.3327629E-02 17.39020 at 10iterations 5.4340912E-03 0.7592163 at 20iterations 5.6426896E-04 9.3997955E-02 at 30iterations 1.5929482E-04 2.3962021E-02 at 40iterations 6.0987022E-05 8.2988739E-03 at 50iterations finished qdiffx linear iterations at : 16:04:29 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.0987022E-05 8.2988739E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 16:04:29 3.444u 0.169s 0:03.89 92.5% 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 Mon Oct 10 2011 at 16:04:30 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4166 !!! WARNING: ASP 607 has a net charge of -2.0000 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: 1.605749 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): -19.67900 31.90700 ymin,ymax (A): -34.63100 29.63200 zmin,zma (A): -26.84700 39.66400 x,y,z range (A): 51.58600 64.26300 66.51100 scale (grids/A): 1.605749 object centre (A): 6.114000 -2.499500 6.408499 number of atom coordinates read : 4166 total number of charged atoms : 4018 net assigned charge : 3.500010 assigned positive charge : 614.5282 centred at (gu) : 92.45810 90.64100 82.82629 assigned negative charge : -611.0309 centred at (gu) : 92.55445 90.77261 82.87418 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 27478 mr = 62181 m= 2734 mr = 18889 m= 89 mr = 1380 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 0.4100000 number of dielectric boundary points 35527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 30645 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) : 0.5352498 object centre at (A) : 6.114000 -2.499500 6.408499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0879244E-02 -1.2598771E-03 midg,1,midg; midg,igrid,midg 1.1792559E-02 1.2420258E-02 1,midg,midg; igrid,midg,midg -5.2152742E-03 9.5476682E-04 gauss-seidel spectral radius is 0.9982378 estimated iterations to convergence 189 setup time was (sec) 0.6300000 now iterating at: 16:04:30 rms-change max change #iterations 3.862397 161.4253 at 10iterations 1.625759 53.38458 at 20iterations 0.6885508 23.05800 at 30iterations 0.2901831 11.33584 at 40iterations 0.1226630 4.134985 at 50iterations 5.2201033E-02 1.738846 at 60iterations 2.2162732E-02 0.6705401 at 70iterations 9.4347727E-03 0.3200321 at 80iterations 4.0724799E-03 0.1339817 at 90iterations 1.8066423E-03 5.9379578E-02 at 100iterations 8.5383398E-04 2.5382996E-02 at 110iterations 4.5561616E-04 1.4347076E-02 at 120iterations finished qdiffx linear iterations at : 16:04:37 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 4.5561616E-04 1.4347076E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 16:04:38 7.830u 0.197s 0:08.38 95.7% 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 16:04:38 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4166 !!! WARNING: ASP 607 has a net charge of -2.0000 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: 2.408624 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): -19.67900 31.90700 ymin,ymax (A): -34.63100 29.63200 zmin,zma (A): -26.84700 39.66400 x,y,z range (A): 51.58600 64.26300 66.51100 scale (grids/A): 2.408624 object centre (A): 6.114000 -2.499500 6.408499 number of atom coordinates read : 4166 total number of charged atoms : 4018 net assigned charge : 3.500010 assigned positive charge : 614.5282 centred at (gu) : 93.68697 90.96101 79.23920 assigned negative charge : -611.0309 centred at (gu) : 93.83173 91.15881 79.31125 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 204532 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34858 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 96277 mr = 152237 m= 26852 mr = 76800 m= 4358 mr = 20091 m= 349 mr = 2835 m= 7 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 4464 time to turn everything in is 1.050000 number of dielectric boundary points 80251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 32104 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) : 1.605749 object centre at (A) : 6.114000 -2.499500 6.408499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9229156 8.9832738E-02 midg,1,midg; midg,igrid,midg 0.1607916 0.3042977 1,midg,midg; igrid,midg,midg -9.5071405E-02 3.2303236E-02 gauss-seidel spectral radius is 0.9991806 estimated iterations to convergence 276 setup time was (sec) 1.290000 now iterating at: 16:04:39 rms-change max change #iterations 10.03607 292.9876 at 10iterations 5.776183 153.9413 at 20iterations 3.304293 73.51620 at 30iterations 1.878803 38.15809 at 40iterations 1.066973 21.48561 at 50iterations 0.6036227 12.17484 at 60iterations 0.3405505 7.697909 at 70iterations 0.1920820 3.653152 at 80iterations 0.1082801 2.189255 at 90iterations 6.0710236E-02 1.150713 at 100iterations 3.4125969E-02 0.6762619 at 110iterations 1.9194661E-02 0.3598061 at 120iterations 1.0780865E-02 0.1989822 at 130iterations 6.0746172E-03 0.1111798 at 140iterations 3.4412441E-03 6.2795639E-02 at 150iterations 1.9652450E-03 3.5146713E-02 at 160iterations 1.1450922E-03 2.1756649E-02 at 170iterations 6.8908383E-04 1.1985779E-02 at 180iterations finished qdiffx linear iterations at : 16:04:51 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 6.8908383E-04 1.1985779E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 16:04:52 12.986u 0.209s 0:13.81 95.4% 0+0k 0+0io 0pf+0w