Tue Oct 11 03:20:08 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 Tue Oct 11 2011 at 03:20:09 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 = 3212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5363547 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 0.5363547 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3073 net assigned charge : -5.999974 assigned positive charge : 481.0407 centred at (gu) : 88.94410 91.58305 92.81198 assigned negative charge : -487.0418 centred at (gu) : 88.97999 91.57293 92.84293 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5822 nv = 96 ne = 84 npr = 66660 no. pairs analyzed = 66660 no. exposed pairs = 3968 no. arc points = 27356 no. surface atoms = 1340 nbur = 1872 mkacc time = 0.1900000 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 = 1.596000 m= 229 mr = 3055 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 2989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2807 ## 405 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1242632E-11 -8.2126411E-10 midg,1,midg; midg,igrid,midg -2.0355315E-10 -2.9206595E-10 1,midg,midg; igrid,midg,midg -8.9692351E-11 -3.2971142E-10 gauss-seidel spectral radius is 0.9820976 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 03:20:10 rms-change max change #iterations 6.9977514E-02 13.43378 at 10iterations 4.5230440E-03 0.7914963 at 20iterations 3.6159714E-04 5.9606552E-02 at 30iterations 4.9670132E-05 9.7413063E-03 at 40iterations 1.0067291E-05 2.0940900E-03 at 50iterations finished qdiffx linear iterations at : 03:20:13 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.0067291E-05 2.0940900E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 03:20:13 4.324u 0.287s 0:04.91 93.6% 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 Tue Oct 11 2011 at 03:20:14 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 = 3212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.609064 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 1.609064 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3073 net assigned charge : -5.999974 assigned positive charge : 481.0407 centred at (gu) : 86.83162 94.74818 98.43473 assigned negative charge : -487.0418 centred at (gu) : 86.93985 94.71810 98.52839 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 64528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19405 mr = 43732 m= 1986 mr = 13441 m= 45 mr = 963 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 294 time to turn everything in is 0.6000000 number of dielectric boundary points 27828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 23415 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) : 0.5363547 object centre at (A) : 85.09100 26.47450 69.22300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4754589E-02 -1.4919286E-02 midg,1,midg; midg,igrid,midg -3.5379708E-03 4.1179620E-03 1,midg,midg; igrid,midg,midg -3.6714349E-03 -5.6678695E-03 gauss-seidel spectral radius is 0.9981372 estimated iterations to convergence 184 setup time was (sec) 0.9200000 now iterating at: 03:20:15 rms-change max change #iterations 3.354094 151.4364 at 10iterations 1.376224 47.52047 at 20iterations 0.5670460 20.59095 at 30iterations 0.2338615 8.551731 at 40iterations 9.6861027E-02 3.508308 at 50iterations 3.9919388E-02 1.480331 at 60iterations 1.6493401E-02 0.6317520 at 70iterations 6.8114800E-03 0.2647629 at 80iterations 2.8235142E-03 0.1034317 at 90iterations 1.1765095E-03 4.4048309E-02 at 100iterations 4.9232389E-04 1.7073631E-02 at 110iterations 2.1063939E-04 7.6043606E-03 at 120iterations finished qdiffx linear iterations at : 03:20:23 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 2.1063939E-04 7.6043606E-03 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.770000 DelPhi exited at 03:20:24 9.771u 0.331s 0:10.49 96.2% 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 Tue Oct 11 2011 at 03:20:24 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 = 3212 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.413596 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): 60.00800 110.1740 ymin,ymax (A): -3.163000 56.11200 zmin,zma (A): 36.03600 102.4100 x,y,z range (A): 50.16600 59.27500 66.37399 scale (grids/A): 2.413596 object centre (A): 85.09100 26.47450 69.22300 number of atom coordinates read : 3212 total number of charged atoms : 3073 net assigned charge : -5.999974 assigned positive charge : 481.0407 centred at (gu) : 85.24729 97.12202 102.6518 assigned negative charge : -487.0418 centred at (gu) : 85.40955 97.07703 102.7926 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 150075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27356 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 68139 mr = 107202 m= 18682 mr = 53870 m= 2990 mr = 14105 m= 187 mr = 1945 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 1.430000 number of dielectric boundary points 62872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 24549 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) : 1.609064 object centre at (A) : 85.09100 26.47450 69.22300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4400958 -0.3754496 midg,1,midg; midg,igrid,midg 3.2866122E-03 0.1770139 1,midg,midg; igrid,midg,midg -4.7501754E-02 -7.8060128E-02 gauss-seidel spectral radius is 0.9991242 estimated iterations to convergence 267 setup time was (sec) 1.770000 now iterating at: 03:20:26 rms-change max change #iterations 8.773310 292.3590 at 10iterations 4.910985 121.6671 at 20iterations 2.726012 60.70719 at 30iterations 1.507095 37.16171 at 40iterations 0.8303322 17.84333 at 50iterations 0.4573659 10.34634 at 60iterations 0.2511131 5.707804 at 70iterations 0.1377896 2.908884 at 80iterations 7.5527646E-02 1.530450 at 90iterations 4.1479860E-02 0.8794498 at 100iterations 2.2663096E-02 0.4853115 at 110iterations 1.2441186E-02 0.2432489 at 120iterations 6.8132547E-03 0.1508789 at 130iterations 3.7339800E-03 8.3246231E-02 at 140iterations 2.0521837E-03 4.3445587E-02 at 150iterations 1.1305597E-03 2.2675514E-02 at 160iterations 6.2961766E-04 1.3261080E-02 at 170iterations 3.5370956E-04 7.2708130E-03 at 180iterations finished qdiffx linear iterations at : 03:20:40 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 3.5370956E-04 7.2708130E-03 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 03:20:41 16.210u 0.369s 0:17.04 97.2% 0+0k 0+0io 0pf+0w