Mon Oct 10 17:01:09 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 17:01:09 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.5946217 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): -25.52800 31.72100 ymin,ymax (A): -10.95100 44.23300 zmin,zma (A): 6.883000 66.75300 x,y,z range (A): 57.24900 55.18400 59.87000 scale (grids/A): 0.5946217 object centre (A): 3.096499 16.64100 36.81800 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271956 assigned positive charge : 480.0416 centred at (gu) : 90.37505 89.29836 90.91916 assigned negative charge : -485.3149 centred at (gu) : 90.44461 89.14440 91.02380 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7536 nv = 96 ne = 84 npr = 63383 no. pairs analyzed = 63383 no. exposed pairs = 4199 no. arc points = 29411 no. surface atoms = 1423 nbur = 1761 mkacc time = 0.1100000 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 = 1.456000 m= 343 mr = 3888 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2300000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2996 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9441 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7597398E-09 -7.2466930E-09 midg,1,midg; midg,igrid,midg -9.1971959E-09 3.4200383E-09 1,midg,midg; igrid,midg,midg 7.9316137E-10 -4.8844679E-09 gauss-seidel spectral radius is 0.9854206 estimated iterations to convergence 68 setup time was (sec) 0.4500000 now iterating at: 17:01:10 rms-change max change #iterations 0.1134629 19.37872 at 10iterations 9.4508529E-03 1.451757 at 20iterations 7.9667702E-04 0.1293259 at 30iterations 6.6972891E-05 1.0101557E-02 at 40iterations 5.6714111E-06 9.8037720E-04 at 50iterations finished qdiffx linear iterations at : 17:01:13 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.6714111E-06 9.8037720E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 17:01:14 3.503u 0.245s 0:04.48 83.4% 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 Mon Oct 10 2011 at 17:01:14 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.783865 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): -25.52800 31.72100 ymin,ymax (A): -10.95100 44.23300 zmin,zma (A): 6.883000 66.75300 x,y,z range (A): 57.24900 55.18400 59.87000 scale (grids/A): 1.783865 object centre (A): 3.096499 16.64100 36.81800 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271956 assigned positive charge : 480.0416 centred at (gu) : 91.12415 87.89418 92.75663 assigned negative charge : -485.3149 centred at (gu) : 91.33337 87.43270 93.07121 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29411 grid for indexing accessible points = 1.400000 m= 26628 mr = 55385 m= 3214 mr = 18427 m= 134 mr = 1702 m= 0 mr = 14 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 776 time to turn everything in is 0.4200000 number of dielectric boundary points 36659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 23700 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) : 0.5946217 object centre at (A) : 3.096499 16.64100 36.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4670877E-02 1.0973005E-02 midg,1,midg; midg,igrid,midg -4.5759723E-02 4.3870490E-03 1,midg,midg; igrid,midg,midg 1.9721059E-02 -4.0784184E-02 gauss-seidel spectral radius is 0.9985127 estimated iterations to convergence 206 setup time was (sec) 0.6800000 now iterating at: 17:01:15 rms-change max change #iterations 4.226684 214.0373 at 10iterations 1.891949 68.54823 at 20iterations 0.8556234 31.35860 at 30iterations 0.3855379 13.18766 at 40iterations 0.1750845 5.614836 at 50iterations 7.9304628E-02 2.366173 at 60iterations 3.5866052E-02 1.129608 at 70iterations 1.6215118E-02 0.5730162 at 80iterations 7.3373211E-03 0.2102890 at 90iterations 3.3243783E-03 0.1031733 at 100iterations 1.5095791E-03 4.6464920E-02 at 110iterations 6.8181340E-04 2.0517349E-02 at 120iterations finished qdiffx linear iterations at : 17:01:23 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 6.8181340E-04 2.0517349E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 17:01:24 9.038u 0.277s 0:10.12 91.8% 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 17:01:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.675798 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): -25.52800 31.72100 ymin,ymax (A): -10.95100 44.23300 zmin,zma (A): 6.883000 66.75300 x,y,z range (A): 57.24900 55.18400 59.87000 scale (grids/A): 2.675798 object centre (A): 3.096499 16.64100 36.81800 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.271956 assigned positive charge : 480.0416 centred at (gu) : 91.68598 86.84084 94.13476 assigned negative charge : -485.3149 centred at (gu) : 92.00012 86.14899 94.60682 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 190573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29411 grid for indexing accessible points = 1.400000 m= 89607 mr = 135350 m= 28073 mr = 70921 m= 5306 mr = 21305 m= 525 mr = 3560 m= 15 mr = 260 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2437 time to turn everything in is 1.070000 number of dielectric boundary points 82703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 24323 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) : 1.783865 object centre at (A) : 3.096499 16.64100 36.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1065668 0.2554858 midg,1,midg; midg,igrid,midg -0.5740898 5.3080507E-02 1,midg,midg; igrid,midg,midg 0.4027896 -0.4635352 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.390000 now iterating at: 17:01:26 rms-change max change #iterations 10.45665 400.0038 at 10iterations 6.144142 151.3113 at 20iterations 3.576738 100.5189 at 30iterations 2.075040 49.37234 at 40iterations 1.199433 29.06381 at 50iterations 0.6916883 14.29887 at 60iterations 0.3978859 7.752891 at 70iterations 0.2290473 4.898687 at 80iterations 0.1311413 2.514898 at 90iterations 7.5427607E-02 1.484629 at 100iterations 4.3197069E-02 0.7772120 at 110iterations 2.4758292E-02 0.4593105 at 120iterations 1.4182688E-02 0.2979665 at 130iterations 8.1278896E-03 0.1526394 at 140iterations 4.6496359E-03 7.7888489E-02 at 150iterations 2.6614589E-03 4.7769547E-02 at 160iterations 1.5237801E-03 2.8523684E-02 at 170iterations 8.7224046E-04 1.6222954E-02 at 180iterations finished qdiffx linear iterations at : 17:01:39 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 8.7224046E-04 1.6222954E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 17:01:40 14.514u 0.299s 0:16.44 90.0% 0+0k 0+0io 0pf+0w