Sun Oct 9 01:48:37 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 Sun Oct 9 2011 at 01:48:37 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: HIT 88 has a net charge of 0.5140 !!! WARNING: GLM 89 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5358782 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 0.5358782 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3269 net assigned charge : 16.42003 assigned positive charge : 507.3394 centred at (gu) : 89.88367 89.66573 90.13422 assigned negative charge : -490.9213 centred at (gu) : 89.82289 89.67401 90.32114 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6632 nv = 96 ne = 84 npr = 64883 no. pairs analyzed = 64883 no. exposed pairs = 4749 no. arc points = 33633 no. surface atoms = 1571 nbur = 1844 mkacc time = 0.1400000 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= 301 mr = 3211 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3320 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5458551E-09 -2.8098127E-10 midg,1,midg; midg,igrid,midg 7.9019691E-10 5.9478544E-10 1,midg,midg; igrid,midg,midg 3.9102410E-10 9.5989050E-10 gauss-seidel spectral radius is 0.9821045 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 01:48:38 rms-change max change #iterations 7.3877610E-02 12.21521 at 10iterations 4.6662050E-03 0.7582607 at 20iterations 3.2460634E-04 5.2580833E-02 at 30iterations 3.4418492E-05 5.5091381E-03 at 40iterations 5.8932574E-06 9.5605850E-04 at 50iterations finished qdiffx linear iterations at : 01:48:40 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 5.8932574E-06 9.5605850E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 01:48:41 3.137u 0.158s 0:03.63 90.3% 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 01:48:41 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: HIT 88 has a net charge of 0.5140 !!! WARNING: GLM 89 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.607635 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 1.607635 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3269 net assigned charge : 16.42003 assigned positive charge : 507.3394 centred at (gu) : 89.64981 88.99640 90.40195 assigned negative charge : -490.9213 centred at (gu) : 89.46835 89.02177 90.96304 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33633 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23106 mr = 48312 m= 2389 mr = 15442 m= 67 mr = 1089 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.5000000 number of dielectric boundary points 34433 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 395 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24973 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) : 0.5358782 object centre at (A) : -19.96450 209.9160 112.3505 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1840168E-02 -1.1962409E-02 midg,1,midg; midg,igrid,midg 2.6026087E-02 2.0193374E-02 1,midg,midg; igrid,midg,midg 1.0094671E-02 1.1462457E-02 gauss-seidel spectral radius is 0.9981971 estimated iterations to convergence 187 setup time was (sec) 0.7800000 now iterating at: 01:48:42 rms-change max change #iterations 3.420430 141.3675 at 10iterations 1.422018 58.94274 at 20iterations 0.5949002 18.87097 at 30iterations 0.2477028 8.868992 at 40iterations 0.1028776 3.495964 at 50iterations 4.2980991E-02 1.516211 at 60iterations 1.7963490E-02 0.5965137 at 70iterations 7.5064823E-03 0.2907445 at 80iterations 3.1342476E-03 0.1114900 at 90iterations 1.3115549E-03 4.1529655E-02 at 100iterations 5.5042142E-04 2.1300793E-02 at 110iterations 2.3110415E-04 7.8597069E-03 at 120iterations finished qdiffx linear iterations at : 01:48:48 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 2.3110415E-04 7.8597069E-03 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 01:48:48 6.866u 0.168s 0:07.65 91.7% 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 01:48:49 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3415 !!! WARNING: HIT 88 has a net charge of 0.5140 !!! WARNING: GLM 89 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.411452 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): -47.32200 7.393000 ymin,ymax (A): 178.7380 241.0940 zmin,zma (A): 79.13400 145.5670 x,y,z range (A): 54.71500 62.35600 66.43301 scale (grids/A): 2.411452 object centre (A): -19.96450 209.9160 112.3505 number of atom coordinates read : 3415 total number of charged atoms : 3269 net assigned charge : 16.42003 assigned positive charge : 507.3394 centred at (gu) : 89.47447 88.49432 90.60250 assigned negative charge : -490.9213 centred at (gu) : 89.20231 88.53246 91.44440 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 171125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33633 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 78598 mr = 118833 m= 22876 mr = 60639 m= 3572 mr = 16853 m= 209 mr = 2235 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1038 time to turn everything in is 1.190000 number of dielectric boundary points 77757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 26117 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) : 1.607635 object centre at (A) : -19.96450 209.9160 112.3505 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1853786 -0.1406016 midg,1,midg; midg,igrid,midg 0.3470494 0.3515840 1,midg,midg; igrid,midg,midg 0.1560355 0.1153454 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 1.470000 now iterating at: 01:48:50 rms-change max change #iterations 8.983172 260.5023 at 10iterations 5.128311 137.4173 at 20iterations 2.909328 67.85667 at 30iterations 1.639522 34.06561 at 40iterations 0.9199188 19.39519 at 50iterations 0.5148289 13.09477 at 60iterations 0.2880333 5.830194 at 70iterations 0.1601040 3.479473 at 80iterations 8.9216657E-02 1.761174 at 90iterations 4.9691834E-02 0.9557648 at 100iterations 2.7592963E-02 0.5605011 at 110iterations 1.5353336E-02 0.2952583 at 120iterations 8.5216025E-03 0.1638641 at 130iterations 4.7255186E-03 8.7098122E-02 at 140iterations 2.6192616E-03 5.4732800E-02 at 150iterations 1.4549576E-03 2.8261185E-02 at 160iterations 8.0799533E-04 1.6853333E-02 at 170iterations 4.4833522E-04 8.6374283E-03 at 180iterations finished qdiffx linear iterations at : 01:49:00 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 4.4833522E-04 8.6374283E-03 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 01:49:00 11.054u 0.191s 0:11.51 97.6% 0+0k 0+0io 0pf+0w