Mon Oct 10 16:21:13 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 Mon Oct 10 2011 at 16:21:13 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5511518 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 0.5511518 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 715.1920 centred at (gu) : 90.45479 89.94844 88.45587 assigned negative charge : -708.2900 centred at (gu) : 90.46098 89.99775 88.46592 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9222 nv = 96 ne = 84 npr = 97061 no. pairs analyzed = 97061 no. exposed pairs = 5723 no. arc points = 38974 no. surface atoms = 1927 nbur = 2808 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 405 mr = 5094 m= 4 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4006 ## 524 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 12214 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4550134E-10 2.7476438E-10 midg,1,midg; midg,igrid,midg 1.1632605E-09 -1.1105924E-10 1,midg,midg; igrid,midg,midg 5.3906013E-10 4.9285642E-10 gauss-seidel spectral radius is 0.9831514 estimated iterations to convergence 63 setup time was (sec) 0.5000000 now iterating at: 16:21:13 rms-change max change #iterations 9.9753439E-02 13.17757 at 10iterations 7.4429847E-03 1.128899 at 20iterations 1.1405010E-03 0.2056656 at 30iterations 4.2505455E-04 6.8073273E-02 at 40iterations 1.8193427E-04 2.4654388E-02 at 50iterations finished qdiffx linear iterations at : 16:21:16 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8193427E-04 2.4654388E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 16:21:17 3.539u 0.174s 0:04.00 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 16:21:17 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 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: 1.653455 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 1.653455 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 715.1920 centred at (gu) : 91.36283 89.84391 85.36594 assigned negative charge : -708.2900 centred at (gu) : 91.38240 89.99283 85.39743 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38974 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 34127 mr = 73737 m= 3743 mr = 24055 m= 125 mr = 1843 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.5000000 number of dielectric boundary points 41920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 35066 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) : 0.5511518 object centre at (A) : -35.31950 -2.589002 3.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0729586E-02 -4.3538571E-03 midg,1,midg; midg,igrid,midg 1.7649345E-02 1.7446125E-02 1,midg,midg; igrid,midg,midg 3.9801048E-03 2.9088208E-03 gauss-seidel spectral radius is 0.9984010 estimated iterations to convergence 198 setup time was (sec) 0.7200000 now iterating at: 16:21:18 rms-change max change #iterations 4.465209 203.5642 at 10iterations 1.966810 60.51099 at 20iterations 0.8669681 25.78754 at 30iterations 0.3818584 11.58169 at 40iterations 0.1680262 5.101879 at 50iterations 7.4074239E-02 2.247164 at 60iterations 3.2866899E-02 0.9230967 at 70iterations 1.4540619E-02 0.4423528 at 80iterations 6.5348819E-03 0.2269173 at 90iterations 3.0013646E-03 8.5161075E-02 at 100iterations 1.4455884E-03 4.6230316E-02 at 110iterations 7.7495456E-04 2.3544312E-02 at 120iterations finished qdiffx linear iterations at : 16:21:25 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 7.7495456E-04 2.3544312E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 16:21:25 8.089u 0.202s 0:08.57 96.6% 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 Mon Oct 10 2011 at 16:21:25 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 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: 2.480183 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 2.480183 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 715.1920 centred at (gu) : 92.04391 89.76544 83.04852 assigned negative charge : -708.2900 centred at (gu) : 92.07336 89.98910 83.09597 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 240697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38974 grid for indexing accessible points = 1.400000 m= 116798 mr = 179815 m= 34983 mr = 93651 m= 5954 mr = 26777 m= 482 mr = 3893 m= 9 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2233 time to turn everything in is 1.240000 number of dielectric boundary points 94555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 36548 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) : 1.653455 object centre at (A) : -35.31950 -2.589002 3.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5401672 -0.1023102 midg,1,midg; midg,igrid,midg 0.1904666 0.3528797 1,midg,midg; igrid,midg,midg 9.4044410E-02 5.1402248E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 1.480000 now iterating at: 16:21:27 rms-change max change #iterations 11.46567 336.3977 at 10iterations 6.758794 150.6319 at 20iterations 3.960639 82.27075 at 30iterations 2.308824 43.21675 at 40iterations 1.340785 25.25197 at 50iterations 0.7776303 14.42576 at 60iterations 0.4492942 7.862170 at 70iterations 0.2590159 4.658772 at 80iterations 0.1491925 2.405994 at 90iterations 8.5685864E-02 1.464007 at 100iterations 4.9207982E-02 0.8814954 at 110iterations 2.8314214E-02 0.4559460 at 120iterations 1.6227566E-02 0.2590714 at 130iterations 9.3142018E-03 0.1495905 at 140iterations 5.3674225E-03 8.9467049E-02 at 150iterations 3.0916864E-03 5.5656433E-02 at 160iterations 1.7888071E-03 2.7954102E-02 at 170iterations 1.0494693E-03 1.7188072E-02 at 180iterations finished qdiffx linear iterations at : 16:21:39 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 1.0494693E-03 1.7188072E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 16:21:39 13.447u 0.231s 0:13.97 97.8% 0+0k 0+0io 0pf+0w