Mon Oct 10 17:00:32 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 17:00:32 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 = 2680 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: 0.5683995 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): 19.23400 81.86600 ymin,ymax (A): 7.185000 52.57300 zmin,zma (A): -43.06800 4.814000 x,y,z range (A): 62.63200 45.38800 47.88200 scale (grids/A): 0.5683995 object centre (A): 50.55000 29.87900 -19.12700 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.4117529E-05 assigned positive charge : 399.7175 centred at (gu) : 89.90764 90.13569 89.20546 assigned negative charge : -399.7184 centred at (gu) : 89.91190 89.99262 89.06074 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5710 nv = 96 ne = 84 npr = 53586 no. pairs analyzed = 53586 no. exposed pairs = 3540 no. arc points = 25368 no. surface atoms = 1193 nbur = 1487 mkacc time = 9.0000004E-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= 232 mr = 2877 m= 0 mr = 8 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1900000 number of dielectric boundary points 3057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7338 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3700149E-09 1.5834759E-09 midg,1,midg; midg,igrid,midg -1.8663959E-09 1.9606159E-09 1,midg,midg; igrid,midg,midg 7.5939852E-11 -3.8888195E-11 gauss-seidel spectral radius is 0.9840088 estimated iterations to convergence 65 setup time was (sec) 0.3700000 now iterating at: 17:00:32 rms-change max change #iterations 8.1052266E-02 15.64481 at 10iterations 5.9847068E-03 1.104286 at 20iterations 4.4178174E-04 6.7180634E-02 at 30iterations 3.3104076E-05 5.9833527E-03 at 40iterations 2.4349154E-06 4.1961670E-04 at 50iterations finished qdiffx linear iterations at : 17:00:35 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.4349154E-06 4.1961670E-04 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:00:36 3.362u 0.183s 0:04.39 80.6% 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 17:00:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2680 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: 1.705199 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): 19.23400 81.86600 ymin,ymax (A): 7.185000 52.57300 zmin,zma (A): -43.06800 4.814000 x,y,z range (A): 62.63200 45.38800 47.88200 scale (grids/A): 1.705199 object centre (A): 50.55000 29.87900 -19.12700 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.4117529E-05 assigned positive charge : 399.7175 centred at (gu) : 89.72240 90.40636 87.61591 assigned negative charge : -399.7184 centred at (gu) : 89.73557 89.97748 87.18214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 62165 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25368 grid for indexing accessible points = 1.400000 m= 19204 mr = 41046 m= 2107 mr = 13006 m= 50 mr = 1052 m= 0 mr = 4 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 825 time to turn everything in is 0.3100000 number of dielectric boundary points 28418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19663 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) : 0.5683995 object centre at (A) : 50.55000 29.87900 -19.12700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3122963E-02 6.1934884E-03 midg,1,midg; midg,igrid,midg -2.4778692E-03 6.2977225E-03 1,midg,midg; igrid,midg,midg 9.6216099E-04 -2.0788938E-03 gauss-seidel spectral radius is 0.9983120 estimated iterations to convergence 193 setup time was (sec) 0.5300000 now iterating at: 17:00:37 rms-change max change #iterations 3.435473 154.4283 at 10iterations 1.466406 56.16701 at 20iterations 0.6288017 23.33343 at 30iterations 0.2708103 11.18282 at 40iterations 0.1165807 4.257502 at 50iterations 4.9802471E-02 1.832710 at 60iterations 2.1447858E-02 0.7272224 at 70iterations 9.1869878E-03 0.3687052 at 80iterations 3.9474405E-03 0.1484966 at 90iterations 1.7025974E-03 5.8087349E-02 at 100iterations 7.3011831E-04 2.4621964E-02 at 110iterations 3.1412835E-04 1.1650085E-02 at 120iterations finished qdiffx linear iterations at : 17:00:44 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 3.1412835E-04 1.1650085E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:00:45 7.639u 0.182s 0:08.63 90.4% 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 Mon Oct 10 2011 at 17:00:45 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 = 2680 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: 2.557798 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): 19.23400 81.86600 ymin,ymax (A): 7.185000 52.57300 zmin,zma (A): -43.06800 4.814000 x,y,z range (A): 62.63200 45.38800 47.88200 scale (grids/A): 2.557798 object centre (A): 50.55000 29.87900 -19.12700 number of atom coordinates read : 2680 total number of charged atoms : 2541 net assigned charge : 2.4117529E-05 assigned positive charge : 399.7175 centred at (gu) : 89.58333 90.60946 86.42383 assigned negative charge : -399.7184 centred at (gu) : 89.60323 89.96626 85.77308 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 144258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25368 grid for indexing accessible points = 1.400000 m= 65585 mr = 100888 m= 19706 mr = 51182 m= 3352 mr = 14660 m= 207 mr = 2168 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 2942 time to turn everything in is 0.7500000 number of dielectric boundary points 64136 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20314 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) : 1.705199 object centre at (A) : 50.55000 29.87900 -19.12700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3289539 0.1015448 midg,1,midg; midg,igrid,midg -3.5508364E-02 6.0530394E-02 1,midg,midg; igrid,midg,midg 7.2777130E-02 0.3472723 gauss-seidel spectral radius is 0.9991766 estimated iterations to convergence 275 setup time was (sec) 0.9700000 now iterating at: 17:00:46 rms-change max change #iterations 8.817793 314.9886 at 10iterations 5.024070 156.9387 at 20iterations 2.848922 76.75975 at 30iterations 1.605274 40.08200 at 40iterations 0.9015633 20.72232 at 50iterations 0.5050097 11.52829 at 60iterations 0.2828413 7.131056 at 70iterations 0.1580320 3.606247 at 80iterations 8.7939113E-02 1.839191 at 90iterations 4.9157307E-02 1.181159 at 100iterations 2.7358230E-02 0.6885691 at 110iterations 1.5241195E-02 0.3283234 at 120iterations 8.4728310E-03 0.1771603 at 130iterations 4.7269845E-03 9.4486237E-02 at 140iterations 2.6288694E-03 5.7365417E-02 at 150iterations 1.4628009E-03 2.9609680E-02 at 160iterations 8.1220211E-04 1.5121460E-02 at 170iterations 4.5331009E-04 9.6931458E-03 at 180iterations finished qdiffx linear iterations at : 17:00:58 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 4.5331009E-04 9.6931458E-03 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 17:00:58 12.375u 0.235s 0:13.21 95.3% 0+0k 0+0io 0pf+0w