Sat Oct 15 15:37:33 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 Sat Oct 15 2011 at 15:37:34 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2113 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7081759 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 0.7081759 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1981 net assigned charge : 5.564012 assigned positive charge : 325.6030 centred at (gu) : 91.11413 89.56362 89.40449 assigned negative charge : -320.0391 centred at (gu) : 91.27058 89.60571 89.34488 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7047 nv = 96 ne = 84 npr = 42660 no. pairs analyzed = 42660 no. exposed pairs = 2524 no. arc points = 17088 no. surface atoms = 860 nbur = 1253 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4062 m= 7 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1619 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9927972E-08 7.0817734E-08 midg,1,midg; midg,igrid,midg 7.6613425E-08 2.5107326E-08 1,midg,midg; igrid,midg,midg 1.0328565E-07 -4.1980275E-08 gauss-seidel spectral radius is 0.9896053 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 15:37:36 rms-change max change #iterations 0.2098356 30.18489 at 10iterations 2.6549652E-02 4.001144 at 20iterations 3.5962281E-03 0.4412231 at 30iterations 5.7881686E-04 7.7697754E-02 at 40iterations 1.3379524E-04 1.9554138E-02 at 50iterations finished qdiffx linear iterations at : 15:37:49 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 1.3379524E-04 1.9554138E-02 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.410000 DelPhi exited at 15:37:51 5.414u 0.476s 0:16.33 36.0% 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 15:37:51 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2113 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.124528 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 2.124528 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1981 net assigned charge : 5.564012 assigned positive charge : 325.6030 centred at (gu) : 93.34233 88.69102 88.21350 assigned negative charge : -320.0391 centred at (gu) : 93.81164 88.81729 88.03463 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 30153 mr = 53737 m= 5923 mr = 22970 m= 550 mr = 3991 m= 12 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 30843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15728 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) : 0.7081759 object centre at (A) : 39.74250 14.98900 44.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6199067E-02 5.3823184E-02 midg,1,midg; midg,igrid,midg 3.3491574E-02 5.5240500E-03 1,midg,midg; igrid,midg,midg 2.6040228E-02 1.8860343E-03 gauss-seidel spectral radius is 0.9988309 estimated iterations to convergence 232 setup time was (sec) 1.010000 now iterating at: 15:37:54 rms-change max change #iterations 4.724410 227.8780 at 10iterations 2.336277 79.64121 at 20iterations 1.157351 38.87707 at 30iterations 0.5756589 16.66074 at 40iterations 0.2866544 8.117184 at 50iterations 0.1421215 4.164140 at 60iterations 7.0617273E-02 2.100948 at 70iterations 3.5186682E-02 1.006403 at 80iterations 1.7609416E-02 0.5222626 at 90iterations 8.8141058E-03 0.2641449 at 100iterations 4.4266046E-03 0.1283493 at 110iterations 2.2746392E-03 6.9480896E-02 at 120iterations finished qdiffx linear iterations at : 15:38:15 total time elapsed so far: 12.98000 # loops : 120 mean,max change (kT/e) : 2.2746392E-03 6.9480896E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 15:38:16 13.165u 0.554s 0:24.62 55.6% 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 Sat Oct 15 2011 at 15:38:16 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2113 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.186792 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 3.186792 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1981 net assigned charge : 5.564012 assigned positive charge : 325.6030 centred at (gu) : 95.01353 88.03651 87.32029 assigned negative charge : -320.0391 centred at (gu) : 95.71746 88.22583 87.05202 start vw surface at 0.1200000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 173373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 94107 mr = 129366 m= 38306 mr = 78514 m= 11133 mr = 31511 m= 2234 mr = 8626 m= 255 mr = 1651 m= 8 mr = 142 m= 0 mr = 2 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 69604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 15848 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) : 2.124528 object centre at (A) : 39.74250 14.98900 44.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3248011 0.3941701 midg,1,midg; midg,igrid,midg 0.2975717 3.0536452E-02 1,midg,midg; igrid,midg,midg 0.2240871 0.2034316 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 2.430000 now iterating at: 15:38:23 rms-change max change #iterations 10.49727 354.5570 at 10iterations 6.208353 140.6457 at 20iterations 3.653893 75.74554 at 30iterations 2.151823 42.11823 at 40iterations 1.263701 24.48758 at 50iterations 0.7430942 15.48118 at 60iterations 0.4349653 7.365523 at 70iterations 0.2547244 4.481167 at 80iterations 0.1493466 2.684193 at 90iterations 8.7381810E-02 1.515514 at 100iterations 5.1309120E-02 0.9636959 at 110iterations 3.0298652E-02 0.5303192 at 120iterations 1.7976226E-02 0.3354068 at 130iterations 1.0838493E-02 0.1960220 at 140iterations 6.7131375E-03 0.1157227 at 150iterations 4.2817676E-03 7.8880310E-02 at 160iterations 2.8824946E-03 5.3028107E-02 at 170iterations 2.0473027E-03 3.7376404E-02 at 180iterations finished qdiffx linear iterations at : 15:39:06 total time elapsed so far: 22.50000 # loops : 180 mean,max change (kT/e) : 2.0473027E-03 3.7376404E-02 energy calculations done at 22.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.66000 DelPhi exited at 15:39:08 22.667u 0.574s 0:52.00 44.6% 0+0k 0+0io 0pf+0w