Sun Oct 9 07:47:48 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 Sun Oct 9 2011 at 07:47:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7081336 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): -15.82300 31.13900 ymin,ymax (A): -19.88500 30.38800 zmin,zma (A): -4.127000 35.88000 x,y,z range (A): 46.96200 50.27300 40.00700 scale (grids/A): 0.7081336 object centre (A): 7.658000 5.251500 15.87650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 89.65548 90.64734 90.43376 assigned negative charge : -327.3089 centred at (gu) : 89.52644 90.74403 90.55437 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7636 nv = 96 ne = 84 npr = 45734 no. pairs analyzed = 45734 no. exposed pairs = 2682 no. arc points = 19501 no. surface atoms = 903 nbur = 1317 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4335 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.2700000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1799 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0595129E-07 -1.3134430E-08 midg,1,midg; midg,igrid,midg 9.0837531E-08 7.9074730E-10 1,midg,midg; igrid,midg,midg -1.7717307E-08 1.1183754E-07 gauss-seidel spectral radius is 0.9896242 estimated iterations to convergence 80 setup time was (sec) 0.4800000 now iterating at: 07:47:49 rms-change max change #iterations 0.2107218 29.54402 at 10iterations 2.6510712E-02 3.428859 at 20iterations 3.1830431E-03 0.3813419 at 30iterations 3.9833074E-04 6.0096741E-02 at 40iterations 4.9331538E-05 7.0781708E-03 at 50iterations finished qdiffx linear iterations at : 07:47:51 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 4.9331538E-05 7.0781708E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 07:47:52 3.088u 0.150s 0:03.51 92.0% 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 Sun Oct 9 2011 at 07:47:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.124401 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): -15.82300 31.13900 ymin,ymax (A): -19.88500 30.38800 zmin,zma (A): -4.127000 35.88000 x,y,z range (A): 46.96200 50.27300 40.00700 scale (grids/A): 2.124401 object centre (A): 7.658000 5.251500 15.87650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 88.96613 91.94181 91.30113 assigned negative charge : -327.3089 centred at (gu) : 88.57922 92.23211 91.66304 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19501 grid for indexing accessible points = 1.400000 m= 32309 mr = 55757 m= 6759 mr = 24757 m= 719 mr = 4655 m= 24 mr = 412 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2810 time to turn everything in is 0.6100000 number of dielectric boundary points 34400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16558 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) : 0.7081336 object centre at (A) : 7.658000 5.251500 15.87650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8761773E-02 1.5636157E-02 midg,1,midg; midg,igrid,midg 4.3203510E-02 4.5937262E-03 1,midg,midg; igrid,midg,midg -1.9913372E-02 3.9741646E-02 gauss-seidel spectral radius is 0.9988516 estimated iterations to convergence 234 setup time was (sec) 0.8800000 now iterating at: 07:47:53 rms-change max change #iterations 4.866213 222.4465 at 10iterations 2.401088 74.33643 at 20iterations 1.198906 35.03730 at 30iterations 0.5996308 18.52412 at 40iterations 0.2983304 9.933310 at 50iterations 0.1485700 5.432480 at 60iterations 7.4210912E-02 2.081957 at 70iterations 3.6960918E-02 1.176941 at 80iterations 1.8388977E-02 0.5337029 at 90iterations 9.1799451E-03 0.2645333 at 100iterations 4.5685242E-03 0.1350880 at 110iterations 2.2798819E-03 6.2561035E-02 at 120iterations finished qdiffx linear iterations at : 07:47:59 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 2.2798819E-03 6.2561035E-02 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 07:47:59 7.042u 0.185s 0:07.51 96.1% 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 07:47:59 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NAP 207 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.186601 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): -15.82300 31.13900 ymin,ymax (A): -19.88500 30.38800 zmin,zma (A): -4.127000 35.88000 x,y,z range (A): 46.96200 50.27300 40.00700 scale (grids/A): 3.186601 object centre (A): 7.658000 5.251500 15.87650 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 6.000018 assigned positive charge : 333.3085 centred at (gu) : 88.44905 92.91273 91.95163 assigned negative charge : -327.3089 centred at (gu) : 87.86887 93.34814 92.49452 start vw surface at 0.1300000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 184441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19501 grid for indexing accessible points = 1.400000 m= 99390 mr = 134118 m= 42567 mr = 82959 m= 12986 mr = 35489 m= 2786 mr = 10326 m= 409 mr = 2045 m= 20 mr = 294 m= 0 mr = 6 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 9577 time to turn everything in is 1.790000 number of dielectric boundary points 77362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 16664 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) : 2.124401 object centre at (A) : 7.658000 5.251500 15.87650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6501943 0.1450165 midg,1,midg; midg,igrid,midg 0.3478701 0.1752817 1,midg,midg; igrid,midg,midg -0.1130630 0.2375652 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 2.080000 now iterating at: 07:48:02 rms-change max change #iterations 10.55244 392.8732 at 10iterations 6.138834 123.9959 at 20iterations 3.579833 66.75459 at 30iterations 2.085914 39.74918 at 40iterations 1.213506 19.96731 at 50iterations 0.7066288 12.96488 at 60iterations 0.4110786 7.569675 at 70iterations 0.2395920 4.125605 at 80iterations 0.1389518 2.233898 at 90iterations 8.0994822E-02 1.390834 at 100iterations 4.7035314E-02 0.8942184 at 110iterations 2.7386164E-02 0.4672623 at 120iterations 1.5947443E-02 0.2572803 at 130iterations 9.2674205E-03 0.1621628 at 140iterations 5.3890459E-03 9.3362808E-02 at 150iterations 3.1388223E-03 5.6257248E-02 at 160iterations 1.8275128E-03 2.8482437E-02 at 170iterations 1.0644428E-03 1.8178940E-02 at 180iterations finished qdiffx linear iterations at : 07:48:11 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 1.0644428E-03 1.8178940E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 07:48:12 12.027u 0.172s 0:12.51 97.4% 0+0k 0+0io 0pf+0w