Sun Oct 9 18:44:17 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 Sun Oct 9 2011 at 18:44:17 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5497899 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 0.5497899 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.621037 assigned positive charge : 817.1839 centred at (gu) : 88.02959 89.08099 89.06875 assigned negative charge : -814.5694 centred at (gu) : 87.88866 89.12218 88.97749 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10311 nv = 96 ne = 84 npr = 107731 no. pairs analyzed = 107731 no. exposed pairs = 6141 no. arc points = 41831 no. surface atoms = 2097 nbur = 3202 mkacc time = 0.2800000 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 = 1.568000 m= 472 mr = 5922 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4228 ## 478 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13673 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3226413E-09 1.1887664E-09 midg,1,midg; midg,igrid,midg 1.0195316E-09 -2.6540081E-10 1,midg,midg; igrid,midg,midg -2.9009430E-09 1.3350813E-09 gauss-seidel spectral radius is 0.9831048 estimated iterations to convergence 63 setup time was (sec) 0.8800000 now iterating at: 18:44:19 rms-change max change #iterations 0.1060459 14.33437 at 10iterations 9.7332047E-03 1.304390 at 20iterations 2.8210718E-03 0.3203983 at 30iterations 1.2605666E-03 0.1504860 at 40iterations 5.8198668E-04 7.2884560E-02 at 50iterations finished qdiffx linear iterations at : 18:44:22 total time elapsed so far: 4.630000 # loops : 50 mean,max change (kT/e) : 5.8198668E-04 7.2884560E-02 energy calculations done at 4.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 18:44:23 4.831u 0.378s 0:05.49 94.7% 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 Sun Oct 9 2011 at 18:44:23 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.649370 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 1.649370 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.621037 assigned positive charge : 817.1839 centred at (gu) : 84.08722 87.24154 87.20451 assigned negative charge : -814.5694 centred at (gu) : 83.66570 87.36656 86.93244 start vw surface at 0.1900000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 115715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 39033 mr = 83937 m= 4558 mr = 28140 m= 132 mr = 2400 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.9400000 number of dielectric boundary points 44945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 39630 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) : 0.5497899 object centre at (A) : 35.56000 22.60250 31.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9738344E-02 1.7581297E-02 midg,1,midg; midg,igrid,midg 2.5040887E-02 7.1697072E-03 1,midg,midg; igrid,midg,midg -2.5982317E-02 1.6348112E-02 gauss-seidel spectral radius is 0.9984251 estimated iterations to convergence 200 setup time was (sec) 1.310000 now iterating at: 18:44:25 rms-change max change #iterations 4.864177 156.1718 at 10iterations 2.160642 67.52698 at 20iterations 0.9563257 26.55928 at 30iterations 0.4261089 11.72604 at 40iterations 0.1886671 5.490349 at 50iterations 8.4436305E-02 2.283020 at 60iterations 3.7924346E-02 1.157200 at 70iterations 1.7465658E-02 0.5406585 at 80iterations 8.4443828E-03 0.2242203 at 90iterations 4.5405081E-03 0.1290665 at 100iterations 2.7982304E-03 7.3231459E-02 at 110iterations 1.9250240E-03 5.1277161E-02 at 120iterations finished qdiffx linear iterations at : 18:44:35 total time elapsed so far: 12.00000 # loops : 120 mean,max change (kT/e) : 1.9250240E-03 5.1277161E-02 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 18:44:36 12.171u 0.444s 0:13.02 96.8% 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 Sun Oct 9 2011 at 18:44:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5299 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.474055 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): 3.184000 67.93600 ymin,ymax (A): -9.127000 54.33200 zmin,zma (A): -1.025000 63.45500 x,y,z range (A): 64.75201 63.45900 64.48000 scale (grids/A): 2.474055 object centre (A): 35.56000 22.60250 31.21500 number of atom coordinates read : 5299 total number of charged atoms : 5164 net assigned charge : 2.621037 assigned positive charge : 817.1839 centred at (gu) : 81.13062 85.86191 85.80644 assigned negative charge : -814.5694 centred at (gu) : 80.49862 86.04973 85.39861 start vw surface at 0.1800000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 269097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 133304 mr = 204354 m= 41113 mr = 108550 m= 7335 mr = 31813 m= 589 mr = 4993 m= 15 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 244 time to turn everything in is 2.390000 number of dielectric boundary points 101447 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 2.550000 number of grid points assigned charge 41264 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) : 1.649370 object centre at (A) : 35.56000 22.60250 31.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4810798 0.3939141 midg,1,midg; midg,igrid,midg 0.2512618 1.2877722E-02 1,midg,midg; igrid,midg,midg -0.5072457 0.1700918 gauss-seidel spectral radius is 0.9992533 estimated iterations to convergence 289 setup time was (sec) 2.760000 now iterating at: 18:44:39 rms-change max change #iterations 12.39556 315.1833 at 10iterations 7.314884 156.3159 at 20iterations 4.282185 83.57012 at 30iterations 2.496523 45.06653 at 40iterations 1.451068 25.63700 at 50iterations 0.8405523 15.70787 at 60iterations 0.4864295 7.745235 at 70iterations 0.2807445 5.001305 at 80iterations 0.1619844 2.534871 at 90iterations 9.3569182E-02 1.400959 at 100iterations 5.3870052E-02 0.9102364 at 110iterations 3.1190231E-02 0.4882126 at 120iterations 1.8154981E-02 0.2798424 at 130iterations 1.0726674E-02 0.1879921 at 140iterations 6.4811292E-03 0.1145954 at 150iterations 4.0960507E-03 7.2631836E-02 at 160iterations 2.7468684E-03 5.2379608E-02 at 170iterations 1.9834824E-03 3.4583092E-02 at 180iterations finished qdiffx linear iterations at : 18:44:57 total time elapsed so far: 20.42000 # loops : 180 mean,max change (kT/e) : 1.9834824E-03 3.4583092E-02 energy calculations done at 20.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.58000 DelPhi exited at 18:44:57 20.584u 0.464s 0:21.34 98.5% 0+0k 0+0io 0pf+0w