Mon Oct 10 00:59:36 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 00:59:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6522057 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): 26.98300 64.50200 ymin,ymax (A): -7.559000 45.57600 zmin,zma (A): 39.85700 94.44100 x,y,z range (A): 37.51900 53.13500 54.58400 scale (grids/A): 0.6522057 object centre (A): 45.74250 19.00850 67.14900 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 4.000005 assigned positive charge : 289.7680 centred at (gu) : 89.93426 88.41759 90.07261 assigned negative charge : -285.7683 centred at (gu) : 90.04491 88.28895 90.16025 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5773 nv = 96 ne = 84 npr = 40881 no. pairs analyzed = 40881 no. exposed pairs = 2452 no. arc points = 17276 no. surface atoms = 840 nbur = 1138 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3256 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6666 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8511569E-08 -2.0496604E-09 midg,1,midg; midg,igrid,midg -1.0079289E-08 1.6935193E-08 1,midg,midg; igrid,midg,midg 2.1767532E-08 -4.7269175E-09 gauss-seidel spectral radius is 0.9877624 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 00:59:37 rms-change max change #iterations 0.1358132 21.89852 at 10iterations 1.3837327E-02 2.269335 at 20iterations 1.4390347E-03 0.2403331 at 30iterations 1.4656977E-04 2.1095276E-02 at 40iterations 1.5285565E-05 2.7160645E-03 at 50iterations finished qdiffx linear iterations at : 00:59:40 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.5285565E-05 2.7160645E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 00:59:41 3.524u 0.196s 0:04.01 92.5% 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 00:59:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 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: 1.956617 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): 26.98300 64.50200 ymin,ymax (A): -7.559000 45.57600 zmin,zma (A): 39.85700 94.44100 x,y,z range (A): 37.51900 53.13500 54.58400 scale (grids/A): 1.956617 object centre (A): 45.74250 19.00850 67.14900 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 4.000005 assigned positive charge : 289.7680 centred at (gu) : 89.80308 85.25277 90.21782 assigned negative charge : -285.7683 centred at (gu) : 90.13497 84.86707 90.48110 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17276 grid for indexing accessible points = 1.400000 m= 24266 mr = 42501 m= 4473 mr = 18736 m= 298 mr = 3037 m= 6 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 313 time to turn everything in is 0.5000000 number of dielectric boundary points 25954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14583 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) : 0.6522057 object centre at (A) : 45.74250 19.00850 67.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0853991E-02 2.9645510E-02 midg,1,midg; midg,igrid,midg -5.1482278E-03 4.0809013E-02 1,midg,midg; igrid,midg,midg 1.5519016E-02 -3.0302301E-03 gauss-seidel spectral radius is 0.9986312 estimated iterations to convergence 214 setup time was (sec) 0.8100000 now iterating at: 00:59:42 rms-change max change #iterations 3.748690 191.2542 at 10iterations 1.754778 68.34943 at 20iterations 0.8208551 31.59980 at 30iterations 0.3831740 14.46127 at 40iterations 0.1793310 5.818671 at 50iterations 8.3648533E-02 3.121150 at 60iterations 3.9177839E-02 1.379956 at 70iterations 1.8332368E-02 0.6105118 at 80iterations 8.5644145E-03 0.3130019 at 90iterations 4.0082615E-03 0.1311150 at 100iterations 1.8819289E-03 6.1632156E-02 at 110iterations 8.7844330E-04 2.8677940E-02 at 120iterations finished qdiffx linear iterations at : 00:59:49 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 8.7844330E-04 2.8677940E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 00:59:49 7.971u 0.248s 0:08.56 95.9% 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 00:59:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1978 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: 2.934926 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): 26.98300 64.50200 ymin,ymax (A): -7.559000 45.57600 zmin,zma (A): 39.85700 94.44100 x,y,z range (A): 37.51900 53.13500 54.58400 scale (grids/A): 2.934926 object centre (A): 45.74250 19.00850 67.14900 number of atom coordinates read : 1978 total number of charged atoms : 1846 net assigned charge : 4.000005 assigned positive charge : 289.7680 centred at (gu) : 89.70463 82.87924 90.32672 assigned negative charge : -285.7683 centred at (gu) : 90.20242 82.30067 90.72169 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 141451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17276 grid for indexing accessible points = 1.400000 m= 75334 mr = 102424 m= 30894 mr = 62872 m= 8092 mr = 26021 m= 1267 mr = 6447 m= 101 mr = 869 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 1021 time to turn everything in is 1.250000 number of dielectric boundary points 58444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 14764 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) : 1.956617 object centre at (A) : 45.74250 19.00850 67.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0738130E-02 0.3187265 midg,1,midg; midg,igrid,midg -0.1450404 0.3836316 1,midg,midg; igrid,midg,midg 0.1286597 -2.5925294E-02 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.570000 now iterating at: 00:59:51 rms-change max change #iterations 8.807549 381.7735 at 10iterations 5.098285 167.4330 at 20iterations 2.943623 77.41532 at 30iterations 1.691024 36.73306 at 40iterations 0.9713161 21.46075 at 50iterations 0.5566825 11.00317 at 60iterations 0.3182062 7.940151 at 70iterations 0.1823381 3.858517 at 80iterations 0.1041143 2.109955 at 90iterations 5.9590586E-02 1.208775 at 100iterations 3.4072116E-02 0.6595173 at 110iterations 1.9472925E-02 0.3549261 at 120iterations 1.1125144E-02 0.2147322 at 130iterations 6.3397633E-03 0.1392493 at 140iterations 3.6185365E-03 6.9000244E-02 at 150iterations 2.0691275E-03 3.8129807E-02 at 160iterations 1.1799745E-03 2.3666382E-02 at 170iterations 6.7406445E-04 1.2964249E-02 at 180iterations finished qdiffx linear iterations at : 01:00:02 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 6.7406445E-04 1.2964249E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 01:00:03 12.844u 0.265s 0:13.44 97.4% 0+0k 0+0io 0pf+0w