Sat Oct 8 14:19:22 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 Sat Oct 8 2011 at 14:19:22 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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: 0.6411642 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): -11.78100 43.74300 ymin,ymax (A): -22.64600 22.35400 zmin,zma (A): -8.640000 46.82000 x,y,z range (A): 55.52400 45.00000 55.46000 scale (grids/A): 0.6411642 object centre (A): 15.98100 -0.1459999 19.09000 number of atom coordinates read : 3065 total number of charged atoms : 2918 net assigned charge : -0.9859949 assigned positive charge : 460.9385 centred at (gu) : 89.06580 89.72688 92.36551 assigned negative charge : -461.9253 centred at (gu) : 89.02904 89.64912 92.26720 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8315 nv = 96 ne = 84 npr = 64323 no. pairs analyzed = 64323 no. exposed pairs = 3515 no. arc points = 24294 no. surface atoms = 1196 nbur = 1869 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4860 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.4100000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2396 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10174 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5807886E-09 2.0480778E-08 midg,1,midg; midg,igrid,midg -1.3694821E-08 8.6942009E-09 1,midg,midg; igrid,midg,midg -8.5685983E-09 2.8192086E-09 gauss-seidel spectral radius is 0.9874300 estimated iterations to convergence 73 setup time was (sec) 0.7000000 now iterating at: 14:19:23 rms-change max change #iterations 0.1627349 25.17738 at 10iterations 1.6238565E-02 2.413392 at 20iterations 1.7417246E-03 0.2114983 at 30iterations 2.3062111E-04 3.0815125E-02 at 40iterations 4.2543605E-05 5.7106018E-03 at 50iterations finished qdiffx linear iterations at : 14:19:26 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 4.2543605E-05 5.7106018E-03 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:19:26 4.196u 0.234s 0:04.72 93.6% 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 Sat Oct 8 2011 at 14:19:27 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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: 1.923493 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): -11.78100 43.74300 ymin,ymax (A): -22.64600 22.35400 zmin,zma (A): -8.640000 46.82000 x,y,z range (A): 55.52400 45.00000 55.46000 scale (grids/A): 1.923493 object centre (A): 15.98100 -0.1459999 19.09000 number of atom coordinates read : 3065 total number of charged atoms : 2918 net assigned charge : -0.9859949 assigned positive charge : 460.9385 centred at (gu) : 87.19674 89.17998 97.09608 assigned negative charge : -461.9253 centred at (gu) : 87.08692 88.94690 96.80103 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 90825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24294 grid for indexing accessible points = 1.400000 m= 33006 mr = 65680 m= 4971 mr = 24890 m= 270 mr = 3059 m= 5 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 35357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22993 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) : 0.6411642 object centre at (A) : 15.98100 -0.1459999 19.09000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7769374E-02 6.0206801E-02 midg,1,midg; midg,igrid,midg 2.0221253E-03 2.1517904E-02 1,midg,midg; igrid,midg,midg -5.7094187E-02 7.0643444E-03 gauss-seidel spectral radius is 0.9986949 estimated iterations to convergence 219 setup time was (sec) 1.090000 now iterating at: 14:19:28 rms-change max change #iterations 4.828979 216.9555 at 10iterations 2.304690 83.58244 at 20iterations 1.098751 33.99988 at 30iterations 0.5249306 14.69870 at 40iterations 0.2494110 7.072540 at 50iterations 0.1193737 3.437908 at 60iterations 5.6922063E-02 1.798044 at 70iterations 2.7190328E-02 0.8280449 at 80iterations 1.3014288E-02 0.4071140 at 90iterations 6.2018177E-03 0.1619740 at 100iterations 2.9683269E-03 9.0606689E-02 at 110iterations 1.4217775E-03 4.0744066E-02 at 120iterations finished qdiffx linear iterations at : 14:19:36 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 1.4217775E-03 4.0744066E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.740000 DelPhi exited at 14:19:37 9.742u 0.302s 0:10.34 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 Sat Oct 8 2011 at 14:19:37 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3065 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 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: 2.885239 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): -11.78100 43.74300 ymin,ymax (A): -22.64600 22.35400 zmin,zma (A): -8.640000 46.82000 x,y,z range (A): 55.52400 45.00000 55.46000 scale (grids/A): 2.885239 object centre (A): 15.98100 -0.1459999 19.09000 number of atom coordinates read : 3065 total number of charged atoms : 2918 net assigned charge : -0.9859949 assigned positive charge : 460.9385 centred at (gu) : 85.79507 88.76976 100.6439 assigned negative charge : -461.9253 centred at (gu) : 85.63026 88.42023 100.2014 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 210407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24294 grid for indexing accessible points = 1.400000 m= 108103 mr = 158772 m= 38360 mr = 90068 m= 8902 mr = 31054 m= 1222 mr = 6663 m= 62 mr = 755 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 79731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 23344 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) : 1.923493 object centre at (A) : 15.98100 -0.1459999 19.09000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5772644E-02 0.8055659 midg,1,midg; midg,igrid,midg 6.7992806E-02 0.2680122 1,midg,midg; igrid,midg,midg -0.6411362 0.1636191 gauss-seidel spectral radius is 0.9992816 estimated iterations to convergence 294 setup time was (sec) 2.400000 now iterating at: 14:19:40 rms-change max change #iterations 11.16849 573.3127 at 10iterations 6.555702 128.4170 at 20iterations 3.827719 66.85870 at 30iterations 2.238655 44.75545 at 40iterations 1.300082 22.44630 at 50iterations 0.7566336 14.17780 at 60iterations 0.4396628 7.453369 at 70iterations 0.2552290 4.179882 at 80iterations 0.1480226 2.487736 at 90iterations 8.5917555E-02 1.359943 at 100iterations 4.9843259E-02 0.8596587 at 110iterations 2.8895780E-02 0.4477019 at 120iterations 1.6774919E-02 0.2737541 at 130iterations 9.7365575E-03 0.1582832 at 140iterations 5.6590764E-03 8.7097168E-02 at 150iterations 3.2914460E-03 5.2398682E-02 at 160iterations 1.9225401E-03 3.1394958E-02 at 170iterations 1.1303923E-03 1.7608643E-02 at 180iterations finished qdiffx linear iterations at : 14:19:54 total time elapsed so far: 16.51000 # loops : 180 mean,max change (kT/e) : 1.1303923E-03 1.7608643E-02 energy calculations done at 16.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 14:19:54 16.691u 0.298s 0:17.29 98.2% 0+0k 0+0io 0pf+0w