Tue Nov 22 14:10:32 PST 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 Nov 22 2011 at 14:10:32 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6939031 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): 78.12800 129.4320 ymin,ymax (A): -8.000000 42.74100 zmin,zma (A): -2.417000 46.74900 x,y,z range (A): 51.30399 50.74100 49.16600 scale (grids/A): 0.6939031 object centre (A): 103.7800 17.37050 22.16600 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 5.000010 assigned positive charge : 290.9100 centred at (gu) : 87.48886 90.06593 91.95168 assigned negative charge : -285.9103 centred at (gu) : 87.39769 90.04445 92.08102 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6547 nv = 96 ne = 84 npr = 40032 no. pairs analyzed = 40032 no. exposed pairs = 2624 no. arc points = 18110 no. surface atoms = 889 nbur = 1071 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 3593 m= 0 mr = 93 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1600000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0471559E-08 -1.7770605E-08 midg,1,midg; midg,igrid,midg 2.4559524E-08 3.9507405E-08 1,midg,midg; igrid,midg,midg 1.2608792E-09 3.7868933E-08 gauss-seidel spectral radius is 0.9891741 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 14:10:33 rms-change max change #iterations 0.1778706 29.81549 at 10iterations 2.0683464E-02 2.664709 at 20iterations 2.4588315E-03 0.3732376 at 30iterations 2.8825735E-04 4.3815613E-02 at 40iterations 3.3835571E-05 5.0830841E-03 at 50iterations finished qdiffx linear iterations at : 14:10:39 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 3.3835571E-05 5.0830841E-03 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:10:40 3.630u 0.229s 0:07.63 50.4% 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 Nov 22 2011 at 14:10:40 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.081709 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): 78.12800 129.4320 ymin,ymax (A): -8.000000 42.74100 zmin,zma (A): -2.417000 46.74900 x,y,z range (A): 51.30399 50.74100 49.16600 scale (grids/A): 2.081709 object centre (A): 103.7800 17.37050 22.16600 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 5.000010 assigned positive charge : 290.9100 centred at (gu) : 82.46667 90.19788 95.85532 assigned negative charge : -285.9103 centred at (gu) : 82.19334 90.13350 96.24334 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18110 grid for indexing accessible points = 1.400000 m= 26881 mr = 46676 m= 5073 mr = 20605 m= 440 mr = 3512 m= 9 mr = 271 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 438 time to turn everything in is 0.3800000 number of dielectric boundary points 30249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14511 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) : 0.6939031 object centre at (A) : 103.7800 17.37050 22.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7761665E-02 3.1368390E-03 midg,1,midg; midg,igrid,midg 7.4115316E-03 1.0380941E-03 1,midg,midg; igrid,midg,midg 4.7695935E-03 5.2036833E-02 gauss-seidel spectral radius is 0.9987770 estimated iterations to convergence 226 setup time was (sec) 0.6200000 now iterating at: 14:10:40 rms-change max change #iterations 4.311439 210.9744 at 10iterations 2.101169 85.86184 at 20iterations 1.024576 34.22956 at 30iterations 0.4989730 15.21391 at 40iterations 0.2424934 8.980269 at 50iterations 0.1181964 3.412796 at 60iterations 5.7556655E-02 2.000347 at 70iterations 2.7975233E-02 0.9469419 at 80iterations 1.3678928E-02 0.4204440 at 90iterations 6.6364310E-03 0.1995573 at 100iterations 3.2487845E-03 0.1008949 at 110iterations 1.5786143E-03 5.3485394E-02 at 120iterations finished qdiffx linear iterations at : 14:10:56 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 1.5786143E-03 5.3485394E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.580000 DelPhi exited at 14:10:57 8.583u 0.240s 0:17.09 51.6% 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 Nov 22 2011 at 14:10:57 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.122564 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): 78.12800 129.4320 ymin,ymax (A): -8.000000 42.74100 zmin,zma (A): -2.417000 46.74900 x,y,z range (A): 51.30399 50.74100 49.16600 scale (grids/A): 3.122564 object centre (A): 103.7800 17.37050 22.16600 number of atom coordinates read : 1960 total number of charged atoms : 1828 net assigned charge : 5.000010 assigned positive charge : 290.9100 centred at (gu) : 78.70005 90.29678 98.78293 assigned negative charge : -285.9103 centred at (gu) : 78.29003 90.20031 99.36510 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 158466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18110 grid for indexing accessible points = 1.400000 m= 83260 mr = 112572 m= 34522 mr = 68952 m= 9569 mr = 28966 m= 1929 mr = 7681 m= 230 mr = 1544 m= 9 mr = 144 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1391 time to turn everything in is 1.100000 number of dielectric boundary points 68123 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 14620 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) : 2.081709 object centre at (A) : 103.7800 17.37050 22.16600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5351071 -6.0981128E-02 midg,1,midg; midg,igrid,midg -4.6798207E-02 -7.1846448E-02 1,midg,midg; igrid,midg,midg -4.2753063E-02 0.4532293 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 298 setup time was (sec) 1.370000 now iterating at: 14:10:59 rms-change max change #iterations 9.869968 519.5443 at 10iterations 5.764054 183.1098 at 20iterations 3.407850 85.21446 at 30iterations 1.996131 50.57858 at 40iterations 1.164884 27.50821 at 50iterations 0.6796117 13.77765 at 60iterations 0.3965124 7.350838 at 70iterations 0.2305302 4.227259 at 80iterations 0.1343695 2.536888 at 90iterations 7.8005850E-02 1.358836 at 100iterations 4.5504242E-02 0.8231525 at 110iterations 2.6449997E-02 0.5041924 at 120iterations 1.5391695E-02 0.2913215 at 130iterations 8.9401305E-03 0.1553116 at 140iterations 5.2065346E-03 9.3551636E-02 at 150iterations 3.0329593E-03 5.1689148E-02 at 160iterations 1.7627761E-03 3.5414934E-02 at 170iterations 1.0247756E-03 1.9405365E-02 at 180iterations finished qdiffx linear iterations at : 14:11:23 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 1.0247756E-03 1.9405365E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 14:11:24 13.822u 0.260s 0:26.67 52.7% 0+0k 0+0io 0pf+0w