Sat Oct 15 15:12:03 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 Sat Oct 15 2011 at 15:12:03 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 = 2803 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6160129 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 0.6160129 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2655 net assigned charge : 4.500027 assigned positive charge : 422.5097 centred at (gu) : 90.24929 89.78717 92.31928 assigned negative charge : -418.0104 centred at (gu) : 90.52445 89.76881 92.26680 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6841 nv = 96 ne = 84 npr = 58285 no. pairs analyzed = 58285 no. exposed pairs = 3352 no. arc points = 23527 no. surface atoms = 1134 nbur = 1669 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3712 m= 0 mr = 36 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 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6962569E-11 1.0879083E-08 midg,1,midg; midg,igrid,midg 2.1034390E-09 4.1431329E-09 1,midg,midg; igrid,midg,midg 1.8988942E-08 -1.5673704E-08 gauss-seidel spectral radius is 0.9863664 estimated iterations to convergence 70 setup time was (sec) 0.4300000 now iterating at: 15:12:04 rms-change max change #iterations 0.1293362 18.14817 at 10iterations 1.1840046E-02 1.692846 at 20iterations 1.1263652E-03 0.1658020 at 30iterations 1.3242931E-04 2.0952225E-02 at 40iterations 3.0377629E-05 5.4321289E-03 at 50iterations finished qdiffx linear iterations at : 15:12:07 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 3.0377629E-05 5.4321289E-03 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 15:12:07 3.788u 0.235s 0:04.41 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 Sat Oct 15 2011 at 15:12:08 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 = 2803 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.848039 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 1.848039 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2655 net assigned charge : 4.500027 assigned positive charge : 422.5097 centred at (gu) : 90.74730 89.36108 96.95739 assigned negative charge : -418.0104 centred at (gu) : 91.57300 89.30612 96.80005 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23527 grid for indexing accessible points = 1.400000 m= 26642 mr = 50711 m= 4121 mr = 19401 m= 207 mr = 2483 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20779 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) : 0.6160129 object centre at (A) : -5.792000 23.23450 16.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4563692E-02 1.8853288E-02 midg,1,midg; midg,igrid,midg 1.1551479E-03 -2.3781715E-03 1,midg,midg; igrid,midg,midg 2.8540056E-02 -1.1655076E-02 gauss-seidel spectral radius is 0.9985689 estimated iterations to convergence 210 setup time was (sec) 0.6200000 now iterating at: 15:12:08 rms-change max change #iterations 4.168911 157.6962 at 10iterations 1.914664 66.63006 at 20iterations 0.8818604 28.89716 at 30iterations 0.4080865 13.82976 at 40iterations 0.1883278 6.295380 at 50iterations 8.6839095E-02 2.716968 at 60iterations 4.0018894E-02 1.209183 at 70iterations 1.8449880E-02 0.5753303 at 80iterations 8.5107554E-03 0.2576103 at 90iterations 3.9194231E-03 0.1196175 at 100iterations 1.8236627E-03 6.0045242E-02 at 110iterations 8.5083582E-04 2.6044846E-02 at 120iterations finished qdiffx linear iterations at : 15:12:16 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 8.5083582E-04 2.6044846E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 15:12:17 8.407u 0.242s 0:09.05 95.4% 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 Sat Oct 15 2011 at 15:12:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2803 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.772058 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): -30.88200 19.29800 ymin,ymax (A): -1.910000 48.37900 zmin,zma (A): -12.53100 45.26000 x,y,z range (A): 50.18000 50.28900 57.79100 scale (grids/A): 2.772058 object centre (A): -5.792000 23.23450 16.36450 number of atom coordinates read : 2803 total number of charged atoms : 2655 net assigned charge : 4.500027 assigned positive charge : 422.5097 centred at (gu) : 91.12085 89.04143 100.4357 assigned negative charge : -418.0104 centred at (gu) : 92.35947 88.95912 100.2001 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 169964 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23527 grid for indexing accessible points = 1.400000 m= 85683 mr = 123098 m= 31112 mr = 69690 m= 7132 mr = 24672 m= 926 mr = 5202 m= 32 mr = 540 m= 0 mr = 1 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 71646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21236 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) : 1.848039 object centre at (A) : -5.792000 23.23450 16.36450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2818365 0.3776703 midg,1,midg; midg,igrid,midg -4.9732622E-02 -9.7592779E-02 1,midg,midg; igrid,midg,midg 0.1980106 -2.1453610E-02 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.250000 now iterating at: 15:12:18 rms-change max change #iterations 9.973334 354.2964 at 10iterations 5.835824 127.4747 at 20iterations 3.407080 88.13506 at 30iterations 1.972855 38.54397 at 40iterations 1.137573 24.25518 at 50iterations 0.6560864 13.62832 at 60iterations 0.3778942 7.703653 at 70iterations 0.2174248 4.402374 at 80iterations 0.1249103 2.193645 at 90iterations 7.1681470E-02 1.503777 at 100iterations 4.1108325E-02 0.7568970 at 110iterations 2.3566050E-02 0.4248676 at 120iterations 1.3544312E-02 0.2469068 at 130iterations 7.7481735E-03 0.1472027 at 140iterations 4.4466634E-03 8.6616069E-02 at 150iterations 2.5527643E-03 4.4930935E-02 at 160iterations 1.4693697E-03 3.2389164E-02 at 170iterations 8.5163646E-04 1.7299652E-02 at 180iterations finished qdiffx linear iterations at : 15:12:31 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 8.5163646E-04 1.7299652E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.18000 DelPhi exited at 15:12:31 14.177u 0.271s 0:14.82 97.4% 0+0k 0+0io 0pf+0w