Tue Oct 11 08:38:13 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 Tue Oct 11 2011 at 08:38:13 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6632140 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 0.6632140 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 412.4378 centred at (gu) : 90.18645 90.47132 88.51046 assigned negative charge : -410.9383 centred at (gu) : 90.42853 90.30576 88.61246 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8025 nv = 96 ne = 84 npr = 55409 no. pairs analyzed = 55409 no. exposed pairs = 3320 no. arc points = 23037 no. surface atoms = 1109 nbur = 1606 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 4605 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3700000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6590404E-08 -1.4290518E-08 midg,1,midg; midg,igrid,midg -3.1158361E-08 4.4974744E-08 1,midg,midg; igrid,midg,midg 5.5155187E-08 -5.4705861E-08 gauss-seidel spectral radius is 0.9882234 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 08:38:14 rms-change max change #iterations 0.1771718 24.90151 at 10iterations 1.9413291E-02 2.508091 at 20iterations 2.2022531E-03 0.3047028 at 30iterations 2.8301167E-04 3.6087036E-02 at 40iterations 5.4413737E-05 7.4348450E-03 at 50iterations finished qdiffx linear iterations at : 08:38:17 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 5.4413737E-05 7.4348450E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 08:38:18 4.172u 0.290s 0:04.75 93.8% 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 Tue Oct 11 2011 at 08:38:18 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.989642 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 1.989642 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 412.4378 centred at (gu) : 90.55880 91.41338 85.53063 assigned negative charge : -410.9383 centred at (gu) : 91.28513 90.91692 85.83698 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 86311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23037 grid for indexing accessible points = 1.400000 m= 32260 mr = 61364 m= 5256 mr = 24266 m= 344 mr = 3369 m= 8 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2362 time to turn everything in is 0.7500000 number of dielectric boundary points 35038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 20302 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) : 0.6632140 object centre at (A) : 8.996500 31.54100 52.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0657514E-02 -5.7028543E-02 midg,1,midg; midg,igrid,midg -1.7037487E-02 3.2367319E-02 1,midg,midg; igrid,midg,midg 7.6891549E-02 -1.6883634E-02 gauss-seidel spectral radius is 0.9987553 estimated iterations to convergence 224 setup time was (sec) 1.070000 now iterating at: 08:38:19 rms-change max change #iterations 4.792126 218.7109 at 10iterations 2.330657 80.81757 at 20iterations 1.129455 35.11784 at 30iterations 0.5483179 16.17677 at 40iterations 0.2671642 7.894832 at 50iterations 0.1293127 3.630521 at 60iterations 6.2899739E-02 1.754058 at 70iterations 3.0595863E-02 0.8375950 at 80iterations 1.4859905E-02 0.4466524 at 90iterations 7.1926084E-03 0.2019148 at 100iterations 3.5083755E-03 0.1090879 at 110iterations 1.7126704E-03 5.1385880E-02 at 120iterations finished qdiffx linear iterations at : 08:38:28 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 1.7126704E-03 5.1385880E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 08:38:28 9.831u 0.328s 0:10.46 97.0% 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 Tue Oct 11 2011 at 08:38:28 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2715 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.984463 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): -15.22300 33.21600 ymin,ymax (A): 7.429000 55.65300 zmin,zma (A): 25.71600 79.39400 x,y,z range (A): 48.43900 48.22400 53.67800 scale (grids/A): 2.984463 object centre (A): 8.996500 31.54100 52.55500 number of atom coordinates read : 2715 total number of charged atoms : 2567 net assigned charge : 1.500014 assigned positive charge : 412.4378 centred at (gu) : 90.83814 92.12011 83.29587 assigned negative charge : -410.9383 centred at (gu) : 91.92762 91.37534 83.75549 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 199467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23037 grid for indexing accessible points = 1.400000 m= 103740 mr = 147915 m= 38688 mr = 86056 m= 9700 mr = 31567 m= 1529 mr = 7512 m= 110 mr = 978 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 7794 time to turn everything in is 1.990000 number of dielectric boundary points 79159 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 20536 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) : 1.989642 object centre at (A) : 8.996500 31.54100 52.55500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3446841 -0.6031237 midg,1,midg; midg,igrid,midg -0.1615186 0.3771888 1,midg,midg; igrid,midg,midg 0.6541726 -0.1349101 gauss-seidel spectral radius is 0.9992837 estimated iterations to convergence 295 setup time was (sec) 2.310000 now iterating at: 08:38:31 rms-change max change #iterations 10.97162 479.0465 at 10iterations 6.446124 153.8202 at 20iterations 3.767363 71.92088 at 30iterations 2.208673 49.47990 at 40iterations 1.293003 22.46007 at 50iterations 0.7541700 13.05137 at 60iterations 0.4397403 9.342217 at 70iterations 0.2562377 4.545046 at 80iterations 0.1490784 2.429182 at 90iterations 8.6858205E-02 1.588234 at 100iterations 5.0611813E-02 0.9142761 at 110iterations 2.9385792E-02 0.5641675 at 120iterations 1.7154530E-02 0.3235502 at 130iterations 1.0028848E-02 0.1609383 at 140iterations 5.8610169E-03 9.6321106E-02 at 150iterations 3.4691328E-03 7.0563793E-02 at 160iterations 2.0663482E-03 3.3466339E-02 at 170iterations 1.2579148E-03 2.3275375E-02 at 180iterations finished qdiffx linear iterations at : 08:38:45 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 1.2579148E-03 2.3275375E-02 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.76000 DelPhi exited at 08:38:46 16.763u 0.341s 0:17.46 97.9% 0+0k 0+0io 0pf+0w