Mon Oct 10 17:04:07 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 Mon Oct 10 2011 at 17:04:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 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: 0.5732228 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 0.5732228 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4999792 assigned positive charge : 418.1743 centred at (gu) : 89.75618 89.28928 89.42216 assigned negative charge : -418.6753 centred at (gu) : 89.75814 89.15122 89.25218 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5822 nv = 96 ne = 84 npr = 56445 no. pairs analyzed = 56445 no. exposed pairs = 3611 no. arc points = 25658 no. surface atoms = 1219 nbur = 1568 mkacc time = 9.9999994E-02 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 = 1.512000 m= 263 mr = 2896 m= 0 mr = 19 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2628 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3456768E-09 2.3531308E-09 midg,1,midg; midg,igrid,midg -2.8056555E-09 1.8512376E-09 1,midg,midg; igrid,midg,midg -1.3636519E-11 -7.3594533E-11 gauss-seidel spectral radius is 0.9842802 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 17:04:08 rms-change max change #iterations 8.9032084E-02 17.69080 at 10iterations 6.8835062E-03 1.224609 at 20iterations 5.3589215E-04 7.9728127E-02 at 30iterations 4.4674201E-05 6.9465637E-03 at 40iterations 4.7280905E-06 8.6402893E-04 at 50iterations finished qdiffx linear iterations at : 17:04:11 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.7280905E-06 8.6402893E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:04:12 3.568u 0.196s 0:04.17 89.9% 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 Mon Oct 10 2011 at 17:04:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 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: 1.719668 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 1.719668 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4999792 assigned positive charge : 418.1743 centred at (gu) : 89.26759 87.86696 88.26581 assigned negative charge : -418.6753 centred at (gu) : 89.27407 87.45351 87.75621 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25658 grid for indexing accessible points = 1.400000 m= 19904 mr = 42471 m= 2258 mr = 13571 m= 58 mr = 1047 m= 0 mr = 6 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 159 time to turn everything in is 0.3200000 number of dielectric boundary points 29414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 281 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20458 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) : 0.5732228 object centre at (A) : 15.96650 35.83700 20.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2109974E-02 1.0464571E-02 midg,1,midg; midg,igrid,midg -6.0680443E-03 6.1110766E-03 1,midg,midg; igrid,midg,midg 1.0832770E-03 6.2713097E-03 gauss-seidel spectral radius is 0.9983489 estimated iterations to convergence 195 setup time was (sec) 0.5300000 now iterating at: 17:04:13 rms-change max change #iterations 3.549359 166.3285 at 10iterations 1.532237 57.12432 at 20iterations 0.6632521 25.59015 at 30iterations 0.2885164 10.19780 at 40iterations 0.1250769 4.707426 at 50iterations 5.4158837E-02 2.118731 at 60iterations 2.3488637E-02 0.8785477 at 70iterations 1.0196876E-02 0.4230423 at 80iterations 4.4149589E-03 0.1525745 at 90iterations 1.9126136E-03 6.8726540E-02 at 100iterations 8.3478860E-04 2.8382301E-02 at 110iterations 3.6166492E-04 1.2858868E-02 at 120iterations finished qdiffx linear iterations at : 17:04:20 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.6166492E-04 1.2858868E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 17:04:21 8.037u 0.233s 0:09.14 90.3% 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 Mon Oct 10 2011 at 17:04:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2787 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: 2.579503 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): -15.08600 47.01900 ymin,ymax (A): 12.20700 59.46700 zmin,zma (A): -2.939000 43.93800 x,y,z range (A): 62.10500 47.26000 46.87700 scale (grids/A): 2.579503 object centre (A): 15.96650 35.83700 20.49950 number of atom coordinates read : 2787 total number of charged atoms : 2647 net assigned charge : -0.4999792 assigned positive charge : 418.1743 centred at (gu) : 88.90109 86.80029 87.39830 assigned negative charge : -418.6753 centred at (gu) : 88.91111 86.18019 86.63426 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 149086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25658 grid for indexing accessible points = 1.400000 m= 67786 mr = 104296 m= 20606 mr = 52883 m= 3501 mr = 15380 m= 269 mr = 2202 m= 8 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 453 time to turn everything in is 0.7900000 number of dielectric boundary points 66376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 21154 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) : 1.719668 object centre at (A) : 15.96650 35.83700 20.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2432831 0.1595199 midg,1,midg; midg,igrid,midg -5.7167932E-02 7.6996200E-02 1,midg,midg; igrid,midg,midg 4.1032992E-02 0.2701628 gauss-seidel spectral radius is 0.9991887 estimated iterations to convergence 277 setup time was (sec) 1.040000 now iterating at: 17:04:22 rms-change max change #iterations 9.117202 345.6142 at 10iterations 5.207111 135.2850 at 20iterations 2.967964 72.57314 at 30iterations 1.676265 41.61490 at 40iterations 0.9475573 25.02470 at 50iterations 0.5324020 12.31281 at 60iterations 0.2997678 6.042574 at 70iterations 0.1683523 3.810917 at 80iterations 9.4333991E-02 2.067859 at 90iterations 5.2985992E-02 1.109368 at 100iterations 2.9662140E-02 0.6273651 at 110iterations 1.6604792E-02 0.3350754 at 120iterations 9.3221823E-03 0.1923065 at 130iterations 5.2148728E-03 0.1127443 at 140iterations 2.9197722E-03 6.0441017E-02 at 150iterations 1.6318521E-03 3.3786774E-02 at 160iterations 9.1584428E-04 1.9154549E-02 at 170iterations 5.1093404E-04 1.0807514E-02 at 180iterations finished qdiffx linear iterations at : 17:04:34 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 5.1093404E-04 1.0807514E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 17:04:35 12.911u 0.228s 0:14.27 92.0% 0+0k 0+0io 0pf+0w