Tue Oct 11 04:30:36 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 04:30:36 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! 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: 0.6563542 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 0.6563542 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8379812 assigned positive charge : 418.0257 centred at (gu) : 90.14824 90.44931 91.53406 assigned negative charge : -418.8643 centred at (gu) : 89.89419 90.33368 91.49584 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7838 nv = 96 ne = 84 npr = 56925 no. pairs analyzed = 56925 no. exposed pairs = 3397 no. arc points = 23361 no. surface atoms = 1148 nbur = 1622 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 439 mr = 4421 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2100000 number of dielectric boundary points 3801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2321 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9494 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9699713E-09 7.3146968E-09 midg,1,midg; midg,igrid,midg -2.2611919E-08 2.2021931E-08 1,midg,midg; igrid,midg,midg -5.1164932E-08 4.7283969E-08 gauss-seidel spectral radius is 0.9879811 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 04:30:37 rms-change max change #iterations 0.1675770 22.58960 at 10iterations 1.8223755E-02 2.463924 at 20iterations 2.0359077E-03 0.2986755 at 30iterations 2.9896863E-04 3.8646698E-02 at 40iterations 7.2019786E-05 8.6288452E-03 at 50iterations finished qdiffx linear iterations at : 04:30:40 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 7.2019786E-05 8.6288452E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 04:30:41 3.408u 0.190s 0:04.34 82.7% 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 Tue Oct 11 2011 at 04:30:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! 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: 1.969063 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 1.969063 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8379812 assigned positive charge : 418.0257 centred at (gu) : 90.44433 91.34731 94.60146 assigned negative charge : -418.8643 centred at (gu) : 89.68233 91.00075 94.48736 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 31774 mr = 60032 m= 5121 mr = 23801 m= 315 mr = 3244 m= 4 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1106 time to turn everything in is 0.4100000 number of dielectric boundary points 35016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20661 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) : 0.6563542 object centre at (A) : 12.71850 -1.589500 18.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0192508E-02 -2.3060856E-02 midg,1,midg; midg,igrid,midg -1.6567424E-02 2.1369075E-02 1,midg,midg; igrid,midg,midg -1.6775994E-02 6.7288972E-02 gauss-seidel spectral radius is 0.9987336 estimated iterations to convergence 223 setup time was (sec) 0.6200000 now iterating at: 04:30:41 rms-change max change #iterations 4.739073 188.1784 at 10iterations 2.285634 74.75262 at 20iterations 1.099096 35.82540 at 30iterations 0.5309224 16.77542 at 40iterations 0.2577544 7.170769 at 50iterations 0.1244550 3.628041 at 60iterations 5.9754267E-02 1.703789 at 70iterations 2.8966973E-02 0.9034338 at 80iterations 1.4007215E-02 0.3999786 at 90iterations 6.7971237E-03 0.2156105 at 100iterations 3.3144613E-03 9.2288971E-02 at 110iterations 1.6269495E-03 4.5175552E-02 at 120iterations finished qdiffx linear iterations at : 04:30:49 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.6269495E-03 4.5175552E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 04:30:49 7.876u 0.213s 0:08.38 96.4% 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 04:30:49 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ASP 29 has a net charge of -2.0000 !!! 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: 2.953594 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): -11.71000 37.14700 ymin,ymax (A): -25.77500 22.59600 zmin,zma (A): -8.833000 45.40600 x,y,z range (A): 48.85700 48.37100 54.23900 scale (grids/A): 2.953594 object centre (A): 12.71850 -1.589500 18.28650 number of atom coordinates read : 2770 total number of charged atoms : 2618 net assigned charge : -0.8379812 assigned positive charge : 418.0257 centred at (gu) : 90.66635 92.02080 96.90212 assigned negative charge : -418.8643 centred at (gu) : 89.52336 91.50101 96.73087 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 196279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23361 grid for indexing accessible points = 1.400000 m= 102159 mr = 144865 m= 38057 mr = 84466 m= 9298 mr = 30875 m= 1300 mr = 6981 m= 98 mr = 869 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 3937 time to turn everything in is 1.090000 number of dielectric boundary points 79092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20938 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) : 1.969063 object centre at (A) : 12.71850 -1.589500 18.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.349917 0.1054131 midg,1,midg; midg,igrid,midg -0.1890775 0.2832360 1,midg,midg; igrid,midg,midg -0.1173230 0.6148983 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.330000 now iterating at: 04:30:51 rms-change max change #iterations 10.88009 341.1814 at 10iterations 6.385717 169.6110 at 20iterations 3.742836 73.07924 at 30iterations 2.191630 42.44706 at 40iterations 1.281610 25.95375 at 50iterations 0.7493231 14.03321 at 60iterations 0.4360708 7.757643 at 70iterations 0.2539703 4.267960 at 80iterations 0.1478933 2.787394 at 90iterations 8.6041316E-02 1.436243 at 100iterations 5.0193101E-02 0.9039383 at 110iterations 2.9294187E-02 0.4723148 at 120iterations 1.7047346E-02 0.3084660 at 130iterations 9.9694775E-03 0.1737671 at 140iterations 5.8682319E-03 0.1043110 at 150iterations 3.5017345E-03 6.5378189E-02 at 160iterations 2.1228031E-03 4.3495178E-02 at 170iterations 1.3226095E-03 2.6836395E-02 at 180iterations finished qdiffx linear iterations at : 04:31:02 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 1.3226095E-03 2.6836395E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 04:31:03 12.932u 0.227s 0:13.78 95.4% 0+0k 0+0io 0pf+0w