Mon Oct 10 23:14:53 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 23:14:53 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 = 2631 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6114107 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 0.6114107 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2515 net assigned charge : 4.500016 assigned positive charge : 399.2207 centred at (gu) : 90.36594 90.00214 89.73539 assigned negative charge : -394.7213 centred at (gu) : 90.16196 89.95383 89.56533 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 51956 no. pairs analyzed = 51956 no. exposed pairs = 3233 no. arc points = 22831 no. surface atoms = 1086 nbur = 1545 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 3675 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3000000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 262 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8175 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7312316E-09 1.0880385E-08 midg,1,midg; midg,igrid,midg 2.2908443E-10 5.3078835E-09 1,midg,midg; igrid,midg,midg -7.5231954E-09 1.4391570E-08 gauss-seidel spectral radius is 0.9861547 estimated iterations to convergence 70 setup time was (sec) 0.5800000 now iterating at: 23:14:54 rms-change max change #iterations 0.1212284 18.72238 at 10iterations 1.1409153E-02 1.750993 at 20iterations 1.4633479E-03 0.3020554 at 30iterations 3.6469623E-04 8.4224701E-02 at 40iterations 1.0287145E-04 2.4948120E-02 at 50iterations finished qdiffx linear iterations at : 23:14:58 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 1.0287145E-04 2.4948120E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 23:14:59 4.416u 0.406s 0:05.39 89.2% 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 23:14:59 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 = 2631 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.834232 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 1.834232 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2515 net assigned charge : 4.500016 assigned positive charge : 399.2207 centred at (gu) : 91.09734 90.00562 89.20555 assigned negative charge : -394.7213 centred at (gu) : 90.48563 89.86114 88.69562 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22831 grid for indexing accessible points = 1.400000 m= 25661 mr = 50191 m= 3630 mr = 19087 m= 130 mr = 2236 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2199 time to turn everything in is 0.5800000 number of dielectric boundary points 30055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19636 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) : 0.6114107 object centre at (A) : 28.28550 12.45100 77.40650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7034461E-03 2.3906970E-02 midg,1,midg; midg,igrid,midg -1.7558705E-02 1.7875396E-02 1,midg,midg; igrid,midg,midg -2.0420926E-02 5.6206841E-02 gauss-seidel spectral radius is 0.9985378 estimated iterations to convergence 207 setup time was (sec) 0.9100000 now iterating at: 23:15:00 rms-change max change #iterations 4.004290 155.7280 at 10iterations 1.817557 61.57616 at 20iterations 0.8278651 27.51478 at 30iterations 0.3770250 12.01238 at 40iterations 0.1717505 5.809624 at 50iterations 7.8627482E-02 2.563614 at 60iterations 3.6215767E-02 1.332279 at 70iterations 1.6584570E-02 0.6044846 at 80iterations 7.7182995E-03 0.2863064 at 90iterations 3.6774778E-03 0.1266479 at 100iterations 1.8374497E-03 7.5199127E-02 at 110iterations 9.8478398E-04 4.3701172E-02 at 120iterations finished qdiffx linear iterations at : 23:15:09 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 9.8478398E-04 4.3701172E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.38000 DelPhi exited at 23:15:10 10.383u 0.453s 0:11.46 94.5% 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 23:15:10 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 = 2631 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.751348 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): 0.9690000 55.60200 ymin,ymax (A): -16.66200 41.56400 zmin,zma (A): 56.52600 98.28700 x,y,z range (A): 54.63300 58.22601 41.76100 scale (grids/A): 2.751348 object centre (A): 28.28550 12.45100 77.40650 number of atom coordinates read : 2631 total number of charged atoms : 2515 net assigned charge : 4.500016 assigned positive charge : 399.2207 centred at (gu) : 91.64594 90.00838 88.80834 assigned negative charge : -394.7213 centred at (gu) : 90.72829 89.79161 88.04341 start vw surface at 0.1200000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 167092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22831 grid for indexing accessible points = 1.400000 m= 84416 mr = 121819 m= 29326 mr = 69617 m= 6445 mr = 23572 m= 655 mr = 4819 m= 15 mr = 361 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 7785 time to turn everything in is 1.490000 number of dielectric boundary points 67757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 20120 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) : 1.834232 object centre at (A) : 28.28550 12.45100 77.40650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5341565E-02 0.2457377 midg,1,midg; midg,igrid,midg -0.1985389 0.3191960 1,midg,midg; igrid,midg,midg -0.1880284 0.8513178 gauss-seidel spectral radius is 0.9992313 estimated iterations to convergence 285 setup time was (sec) 1.830000 now iterating at: 23:15:12 rms-change max change #iterations 9.510507 329.8815 at 10iterations 5.467667 128.2253 at 20iterations 3.130561 68.48019 at 30iterations 1.787626 36.61002 at 40iterations 1.018500 20.37209 at 50iterations 0.5805731 11.39449 at 60iterations 0.3308401 6.524517 at 70iterations 0.1883526 3.462219 at 80iterations 0.1071934 2.286135 at 90iterations 6.0878512E-02 1.205825 at 100iterations 3.4651905E-02 0.6186352 at 110iterations 1.9729195E-02 0.3926544 at 120iterations 1.1241464E-02 0.2333107 at 130iterations 6.4534866E-03 0.1279297 at 140iterations 3.7059006E-03 8.0898285E-02 at 150iterations 2.1647341E-03 4.5379639E-02 at 160iterations 1.2952996E-03 2.8968811E-02 at 170iterations 8.0692861E-04 1.9432068E-02 at 180iterations finished qdiffx linear iterations at : 23:15:28 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 8.0692861E-04 1.9432068E-02 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.39000 DelPhi exited at 23:15:28 17.392u 0.461s 0:18.21 98.0% 0+0k 0+0io 0pf+0w