Tue Oct 11 01:12:19 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 Tue Oct 11 2011 at 01:12:19 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 = 2814 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6095995 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 0.6095995 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2669 net assigned charge : 5.500018 assigned positive charge : 425.3623 centred at (gu) : 89.57449 90.13757 89.43642 assigned negative charge : -419.8631 centred at (gu) : 89.79467 90.06648 89.47126 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6897 nv = 96 ne = 84 npr = 57166 no. pairs analyzed = 57166 no. exposed pairs = 3295 no. arc points = 23134 no. surface atoms = 1117 nbur = 1697 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3902 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.3600000 number of dielectric boundary points 3262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6467591E-09 1.1596221E-09 midg,1,midg; midg,igrid,midg -6.2008981E-10 7.0943886E-09 1,midg,midg; igrid,midg,midg 1.5977493E-08 -7.9747737E-09 gauss-seidel spectral radius is 0.9860832 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 01:12:19 rms-change max change #iterations 0.1194855 17.74579 at 10iterations 1.1191833E-02 1.924660 at 20iterations 1.4196831E-03 0.2682877 at 30iterations 2.9712124E-04 6.9732666E-02 at 40iterations 7.7785735E-05 1.8703461E-02 at 50iterations finished qdiffx linear iterations at : 01:12:23 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 7.7785735E-05 1.8703461E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 01:12:23 4.143u 0.295s 0:04.88 90.7% 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 Oct 11 2011 at 01:12:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2814 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.828798 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 1.828798 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2669 net assigned charge : 5.500018 assigned positive charge : 425.3623 centred at (gu) : 88.72278 90.41195 88.30840 assigned negative charge : -419.8631 centred at (gu) : 89.38362 90.19907 88.41331 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 75280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23134 grid for indexing accessible points = 1.400000 m= 26049 mr = 53083 m= 3575 mr = 19352 m= 173 mr = 2307 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 7350 time to turn everything in is 0.6300000 number of dielectric boundary points 30286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20880 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) : 0.6095995 object centre at (A) : 24.03750 7.039001 83.32401 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0560553E-04 4.7237547E-03 midg,1,midg; midg,igrid,midg 1.0170042E-02 1.4148276E-02 1,midg,midg; igrid,midg,midg 4.6838868E-02 -1.5483985E-02 gauss-seidel spectral radius is 0.9985385 estimated iterations to convergence 207 setup time was (sec) 0.9200000 now iterating at: 01:12:25 rms-change max change #iterations 4.131180 186.3471 at 10iterations 1.881063 62.72607 at 20iterations 0.8568534 28.61188 at 30iterations 0.3919012 13.98817 at 40iterations 0.1785627 5.277479 at 50iterations 8.1683904E-02 2.811726 at 60iterations 3.7422299E-02 1.141991 at 70iterations 1.7241867E-02 0.5607648 at 80iterations 7.9828789E-03 0.2534180 at 90iterations 3.7650717E-03 0.1377602 at 100iterations 1.8172116E-03 6.8059921E-02 at 110iterations 9.2449266E-04 4.2598724E-02 at 120iterations finished qdiffx linear iterations at : 01:12:33 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 9.2449266E-04 4.2598724E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 01:12:34 9.535u 0.349s 0:10.47 94.2% 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 Oct 11 2011 at 01:12:34 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 = 2814 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.743197 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): -5.162000 53.23700 ymin,ymax (A): -15.92000 29.99800 zmin,zma (A): 57.25100 109.3970 x,y,z range (A): 58.39900 45.91800 52.14600 scale (grids/A): 2.743197 object centre (A): 24.03750 7.039001 83.32401 number of atom coordinates read : 2814 total number of charged atoms : 2669 net assigned charge : 5.500018 assigned positive charge : 425.3623 centred at (gu) : 88.08380 90.61768 87.46255 assigned negative charge : -419.8631 centred at (gu) : 89.07544 90.29846 87.61990 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 174797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23134 grid for indexing accessible points = 1.400000 m= 86318 mr = 128751 m= 28986 mr = 71185 m= 6496 mr = 23489 m= 752 mr = 5031 m= 26 mr = 511 m= 0 mr = 11 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 24837 time to turn everything in is 1.650000 number of dielectric boundary points 68397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 21351 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) : 1.828798 object centre at (A) : 24.03750 7.039001 83.32401 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6283729E-02 6.1584188E-04 midg,1,midg; midg,igrid,midg 0.1611073 0.1640334 1,midg,midg; igrid,midg,midg 0.6103742 -0.1725814 gauss-seidel spectral radius is 0.9992300 estimated iterations to convergence 284 setup time was (sec) 1.970000 now iterating at: 01:12:36 rms-change max change #iterations 9.684480 358.9890 at 10iterations 5.549187 126.6802 at 20iterations 3.163766 66.25428 at 30iterations 1.803955 35.48847 at 40iterations 1.024648 23.16852 at 50iterations 0.5831968 10.53329 at 60iterations 0.3309008 6.267757 at 70iterations 0.1876976 3.628393 at 80iterations 0.1070381 1.997917 at 90iterations 6.0840838E-02 1.125782 at 100iterations 3.4510978E-02 0.6204834 at 110iterations 1.9680830E-02 0.3809385 at 120iterations 1.1312773E-02 0.2189178 at 130iterations 6.5270583E-03 0.1274719 at 140iterations 3.8231472E-03 8.7673187E-02 at 150iterations 2.2933630E-03 5.4309845E-02 at 160iterations 1.4290006E-03 3.4030914E-02 at 170iterations 9.3822536E-04 2.3807526E-02 at 180iterations finished qdiffx linear iterations at : 01:12:50 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 9.3822536E-04 2.3807526E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.97000 DelPhi exited at 01:12:51 15.975u 0.328s 0:16.59 98.1% 0+0k 0+0io 0pf+0w