Tue Oct 11 08:41:55 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 08:41:55 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIQ 43 has a net charge of 0.5140 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6585641 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 0.6585641 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.970023 assigned positive charge : 421.9917 centred at (gu) : 89.94745 90.26601 91.29265 assigned negative charge : -418.0223 centred at (gu) : 89.69340 90.06640 91.24924 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 57126 no. pairs analyzed = 57126 no. exposed pairs = 3380 no. arc points = 23122 no. surface atoms = 1136 nbur = 1626 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 4437 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3300000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9516 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0479266E-10 2.4158362E-08 midg,1,midg; midg,igrid,midg -3.0435594E-08 5.2548014E-08 1,midg,midg; igrid,midg,midg -4.4460393E-08 5.9661417E-08 gauss-seidel spectral radius is 0.9880588 estimated iterations to convergence 75 setup time was (sec) 0.5500000 now iterating at: 08:41:56 rms-change max change #iterations 0.1726897 23.43911 at 10iterations 1.8334517E-02 2.554115 at 20iterations 2.1003673E-03 0.3074169 at 30iterations 3.0071064E-04 4.2274475E-02 at 40iterations 6.8301335E-05 1.0829926E-02 at 50iterations finished qdiffx linear iterations at : 08:41:58 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 6.8301335E-05 1.0829926E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:41:59 3.373u 0.162s 0:03.88 90.9% 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 08:41:59 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIQ 43 has a net charge of 0.5140 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 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: 1.975692 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 1.975692 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.970023 assigned positive charge : 421.9917 centred at (gu) : 89.84177 90.79743 93.87748 assigned negative charge : -418.0223 centred at (gu) : 89.07964 90.19917 93.74710 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23122 grid for indexing accessible points = 1.400000 m= 32158 mr = 59862 m= 5438 mr = 23924 m= 394 mr = 3584 m= 1 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1131 time to turn everything in is 0.6200000 number of dielectric boundary points 35287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20625 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) : 0.6585641 object centre at (A) : 13.24150 -2.880000 18.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1806517E-02 1.4082530E-02 midg,1,midg; midg,igrid,midg -1.8360307E-02 3.7888184E-02 1,midg,midg; igrid,midg,midg -1.2803222E-02 6.8858467E-02 gauss-seidel spectral radius is 0.9987409 estimated iterations to convergence 223 setup time was (sec) 0.9000000 now iterating at: 08:42:00 rms-change max change #iterations 4.783164 302.0811 at 10iterations 2.318635 68.68236 at 20iterations 1.119287 32.63316 at 30iterations 0.5403185 15.26328 at 40iterations 0.2614833 7.407793 at 50iterations 0.1265215 3.719425 at 60iterations 6.1067607E-02 1.804650 at 70iterations 2.9536003E-02 0.8703032 at 80iterations 1.4344124E-02 0.4033928 at 90iterations 6.9454401E-03 0.2001057 at 100iterations 3.3928840E-03 0.1068985 at 110iterations 1.6457611E-03 5.4134369E-02 at 120iterations finished qdiffx linear iterations at : 08:42:07 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 1.6457611E-03 5.4134369E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 08:42:07 7.548u 0.163s 0:08.12 94.8% 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 Tue Oct 11 2011 at 08:42:07 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIQ 43 has a net charge of 0.5140 !!! WARNING: LEU 262 has a net charge of -0.2720 !!! WARNING: ILE 289 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.963539 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): -10.61300 37.09600 ymin,ymax (A): -27.04800 21.28800 zmin,zma (A): -8.677000 45.38000 x,y,z range (A): 47.70900 48.33600 54.05700 scale (grids/A): 2.963539 object centre (A): 13.24150 -2.880000 18.35150 number of atom coordinates read : 2762 total number of charged atoms : 2613 net assigned charge : 3.970023 assigned positive charge : 421.9917 centred at (gu) : 89.76241 91.19610 95.81612 assigned negative charge : -418.0223 centred at (gu) : 88.61942 90.29868 95.62045 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 196260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23122 grid for indexing accessible points = 1.400000 m= 102281 mr = 144979 m= 38987 mr = 84210 m= 9985 mr = 31731 m= 1585 mr = 7610 m= 122 mr = 1142 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 3662 time to turn everything in is 1.600000 number of dielectric boundary points 79479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 20903 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) : 1.975692 object centre at (A) : 13.24150 -2.880000 18.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5033647 0.3668590 midg,1,midg; midg,igrid,midg -0.2071389 0.4010749 1,midg,midg; igrid,midg,midg -8.6810447E-02 0.6179916 gauss-seidel spectral radius is 0.9992857 estimated iterations to convergence 295 setup time was (sec) 1.900000 now iterating at: 08:42:09 rms-change max change #iterations 11.01431 413.0786 at 10iterations 6.493220 140.8581 at 20iterations 3.820453 92.98418 at 30iterations 2.239671 47.61143 at 40iterations 1.308779 25.35200 at 50iterations 0.7665087 18.42122 at 60iterations 0.4478320 7.977466 at 70iterations 0.2609168 4.517278 at 80iterations 0.1521464 2.520556 at 90iterations 8.8612318E-02 1.510298 at 100iterations 5.1785003E-02 0.9086552 at 110iterations 3.0237287E-02 0.5533962 at 120iterations 1.7673459E-02 0.2845435 at 130iterations 1.0348299E-02 0.1803226 at 140iterations 6.0948869E-03 0.1067886 at 150iterations 3.6378226E-03 6.7699432E-02 at 160iterations 2.2102131E-03 4.2266846E-02 at 170iterations 1.3757260E-03 2.6168823E-02 at 180iterations finished qdiffx linear iterations at : 08:42:21 total time elapsed so far: 13.78000 # loops : 180 mean,max change (kT/e) : 1.3757260E-03 2.6168823E-02 energy calculations done at 13.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.97000 DelPhi exited at 08:42:22 13.975u 0.198s 0:14.54 97.3% 0+0k 0+0io 0pf+0w