Mon Oct 10 14:07:26 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 14:07:26 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 = 2272 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: 0.6874710 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): -20.41600 31.36800 ymin,ymax (A): -58.40200 -12.43800 zmin,zma (A): -8.156000 42.04200 x,y,z range (A): 51.78400 45.96400 50.19800 scale (grids/A): 0.6874710 object centre (A): 5.476000 -35.42000 16.94300 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -4.499990 assigned positive charge : 340.4624 centred at (gu) : 89.32084 89.25346 89.59422 assigned negative charge : -344.9629 centred at (gu) : 89.52457 89.22703 89.53985 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7565 nv = 96 ne = 84 npr = 45620 no. pairs analyzed = 45620 no. exposed pairs = 2987 no. arc points = 21059 no. surface atoms = 1016 nbur = 1256 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4125 m= 7 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1894 ## 129 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6100208E-08 -4.6667012E-09 midg,1,midg; midg,igrid,midg -3.7997708E-08 -1.2656168E-08 1,midg,midg; igrid,midg,midg 5.2300226E-08 -8.3307562E-08 gauss-seidel spectral radius is 0.9890080 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 14:07:27 rms-change max change #iterations 0.1840421 26.20818 at 10iterations 2.1365399E-02 2.774549 at 20iterations 2.4970691E-03 0.3499403 at 30iterations 2.9133307E-04 4.1648865E-02 at 40iterations 3.4219676E-05 4.8542023E-03 at 50iterations finished qdiffx linear iterations at : 14:07:30 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.4219676E-05 4.8542023E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 14:07:31 3.367u 0.147s 0:04.18 83.7% 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 Mon Oct 10 2011 at 14:07:31 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 = 2272 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.062413 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): -20.41600 31.36800 ymin,ymax (A): -58.40200 -12.43800 zmin,zma (A): -8.156000 42.04200 x,y,z range (A): 51.78400 45.96400 50.19800 scale (grids/A): 2.062413 object centre (A): 5.476000 -35.42000 16.94300 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -4.499990 assigned positive charge : 340.4624 centred at (gu) : 87.96217 87.76004 88.78221 assigned negative charge : -344.9629 centred at (gu) : 88.57368 87.68101 88.61960 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 79867 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 31514 mr = 54944 m= 6410 mr = 23438 m= 604 mr = 4283 m= 18 mr = 314 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 35434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 16972 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) : 0.6874710 object centre at (A) : 5.476000 -35.42000 16.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3041520E-02 -2.7872546E-02 midg,1,midg; midg,igrid,midg -1.0187422E-02 -1.0109590E-02 1,midg,midg; igrid,midg,midg -1.2444560E-03 -1.6157925E-02 gauss-seidel spectral radius is 0.9988070 estimated iterations to convergence 229 setup time was (sec) 0.9400000 now iterating at: 14:07:32 rms-change max change #iterations 4.645958 226.6568 at 10iterations 2.264198 89.12981 at 20iterations 1.117220 35.46110 at 30iterations 0.5481536 17.05485 at 40iterations 0.2695575 8.059135 at 50iterations 0.1326347 3.698946 at 60iterations 6.5368153E-02 1.935422 at 70iterations 3.2082308E-02 0.9702358 at 80iterations 1.5753755E-02 0.4427757 at 90iterations 7.7708219E-03 0.2296963 at 100iterations 3.8222258E-03 0.1299992 at 110iterations 1.8794301E-03 5.3903580E-02 at 120iterations finished qdiffx linear iterations at : 14:07:38 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.8794301E-03 5.3903580E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 14:07:40 7.800u 0.188s 0:09.41 84.8% 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 14:07:40 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 = 2272 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: 3.093620 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): -20.41600 31.36800 ymin,ymax (A): -58.40200 -12.43800 zmin,zma (A): -8.156000 42.04200 x,y,z range (A): 51.78400 45.96400 50.19800 scale (grids/A): 3.093620 object centre (A): 5.476000 -35.42000 16.94300 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -4.499990 assigned positive charge : 340.4624 centred at (gu) : 86.94315 86.63991 88.17326 assigned negative charge : -344.9629 centred at (gu) : 87.86052 86.52138 87.92934 start vw surface at 0.1800000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 184208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 97065 mr = 132796 m= 39958 mr = 79640 m= 12067 mr = 32510 m= 2461 mr = 9331 m= 252 mr = 1785 m= 9 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 79814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 17108 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) : 2.062413 object centre at (A) : 5.476000 -35.42000 16.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1849399 -0.5608881 midg,1,midg; midg,igrid,midg 4.9349781E-02 -4.6167821E-03 1,midg,midg; igrid,midg,midg -0.3900366 -9.8832242E-02 gauss-seidel spectral radius is 0.9993011 estimated iterations to convergence 298 setup time was (sec) 2.290000 now iterating at: 14:07:43 rms-change max change #iterations 10.57844 397.3120 at 10iterations 6.302201 168.8810 at 20iterations 3.747092 90.49540 at 30iterations 2.227093 41.64468 at 40iterations 1.312882 25.83316 at 50iterations 0.7723790 14.89430 at 60iterations 0.4560139 8.080844 at 70iterations 0.2682722 4.688966 at 80iterations 0.1570567 2.693362 at 90iterations 9.2140265E-02 1.809381 at 100iterations 5.3978126E-02 0.9172828 at 110iterations 3.1642839E-02 0.5331010 at 120iterations 1.8517936E-02 0.3104162 at 130iterations 1.0812512E-02 0.1804231 at 140iterations 6.3414257E-03 0.1106014 at 150iterations 3.7086525E-03 6.8325043E-02 at 160iterations 2.1755355E-03 3.7586212E-02 at 170iterations 1.2741757E-03 2.2848129E-02 at 180iterations finished qdiffx linear iterations at : 14:07:54 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.2741757E-03 2.2848129E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 14:07:54 13.060u 0.222s 0:14.01 94.7% 0+0k 0+0io 0pf+0w