Sat Oct 8 11:39:12 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 Sat Oct 8 2011 at 11:39:12 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5651062 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 0.5651062 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 469.4153 centred at (gu) : 89.49014 92.53643 91.15427 assigned negative charge : -471.9167 centred at (gu) : 89.41856 92.63269 91.05553 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6882 nv = 96 ne = 84 npr = 62500 no. pairs analyzed = 62500 no. exposed pairs = 4574 no. arc points = 33450 no. surface atoms = 1522 nbur = 1696 mkacc time = 0.2100000 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 = 1.512000 m= 273 mr = 3110 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3223 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 8715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2751326E-09 1.4253120E-09 midg,1,midg; midg,igrid,midg 5.5805954E-10 -3.0726217E-09 1,midg,midg; igrid,midg,midg -1.4666410E-09 6.1555161E-10 gauss-seidel spectral radius is 0.9838827 estimated iterations to convergence 65 setup time was (sec) 0.8000000 now iterating at: 11:39:13 rms-change max change #iterations 8.8514358E-02 14.11265 at 10iterations 6.3807755E-03 1.161915 at 20iterations 4.5670758E-04 7.7236176E-02 at 30iterations 3.4686036E-05 5.3024292E-03 at 40iterations 2.8372178E-06 4.1198730E-04 at 50iterations finished qdiffx linear iterations at : 11:39:17 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 2.8372178E-06 4.1198730E-04 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 11:39:17 4.543u 0.400s 0:05.23 94.4% 0+0k 0+0io 1pf+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 11:39:18 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.695319 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 1.695319 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 469.4153 centred at (gu) : 88.46925 97.60816 93.46155 assigned negative charge : -471.9167 centred at (gu) : 88.25538 97.89751 93.16621 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 75392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33450 grid for indexing accessible points = 1.400000 m= 21306 mr = 47317 m= 2009 mr = 13386 m= 48 mr = 792 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 37260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23623 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) : 0.5651062 object centre at (A) : 37.88150 -7.119498 -20.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0210544E-02 1.2756953E-02 midg,1,midg; midg,igrid,midg 4.9598310E-03 -1.0151098E-02 1,midg,midg; igrid,midg,midg -1.2732411E-02 3.8114775E-03 gauss-seidel spectral radius is 0.9983661 estimated iterations to convergence 196 setup time was (sec) 1.080000 now iterating at: 11:39:19 rms-change max change #iterations 3.715914 153.0673 at 10iterations 1.612263 61.07632 at 20iterations 0.6960247 23.11157 at 30iterations 0.3024822 11.18563 at 40iterations 0.1311208 4.312286 at 50iterations 5.6839060E-02 1.729006 at 60iterations 2.4781222E-02 0.8054543 at 70iterations 1.0791735E-02 0.3722248 at 80iterations 4.6885130E-03 0.1611278 at 90iterations 2.0411285E-03 7.1973801E-02 at 100iterations 8.9195860E-04 3.5564423E-02 at 110iterations 3.8824993E-04 1.2998581E-02 at 120iterations finished qdiffx linear iterations at : 11:39:28 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 3.8824993E-04 1.2998581E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.34000 DelPhi exited at 11:39:29 10.349u 0.464s 0:11.12 97.1% 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 11:39:29 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 = 3218 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.542978 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): 6.383000 69.38000 ymin,ymax (A): -38.13800 23.89900 zmin,zma (A): -47.69400 6.306000 x,y,z range (A): 62.99701 62.03699 54.00000 scale (grids/A): 2.542978 object centre (A): 37.88150 -7.119498 -20.69400 number of atom coordinates read : 3218 total number of charged atoms : 3061 net assigned charge : -2.499993 assigned positive charge : 469.4153 centred at (gu) : 87.70354 101.4119 95.19202 assigned negative charge : -471.9167 centred at (gu) : 87.38287 101.8462 94.74925 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 174968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33450 grid for indexing accessible points = 1.400000 m= 73968 mr = 117230 m= 19878 mr = 55246 m= 2970 mr = 13886 m= 187 mr = 1665 m= 0 mr = 48 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 83896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 24463 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) : 1.695319 object centre at (A) : 37.88150 -7.119498 -20.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1152674 0.1939799 midg,1,midg; midg,igrid,midg 4.0717710E-02 -7.4240685E-02 1,midg,midg; igrid,midg,midg -0.1196913 -4.6583447E-03 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 2.240000 now iterating at: 11:39:31 rms-change max change #iterations 9.652440 369.6355 at 10iterations 5.719340 145.4653 at 20iterations 3.348706 74.87585 at 30iterations 1.946326 42.32189 at 40iterations 1.121794 24.18653 at 50iterations 0.6454167 15.33818 at 60iterations 0.3704128 7.868355 at 70iterations 0.2120114 4.483459 at 80iterations 0.1211285 2.553776 at 90iterations 6.8910375E-02 1.587975 at 100iterations 3.9321236E-02 0.7889481 at 110iterations 2.2327660E-02 0.4339108 at 120iterations 1.2688958E-02 0.2551880 at 130iterations 7.1941507E-03 0.1401024 at 140iterations 4.0795743E-03 8.2771301E-02 at 150iterations 2.3155550E-03 4.5864105E-02 at 160iterations 1.3147654E-03 2.4411857E-02 at 170iterations 7.4733846E-04 1.4822483E-02 at 180iterations finished qdiffx linear iterations at : 11:39:47 total time elapsed so far: 17.50000 # loops : 180 mean,max change (kT/e) : 7.4733846E-04 1.4822483E-02 energy calculations done at 17.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 11:39:47 17.710u 0.483s 0:18.47 98.4% 0+0k 0+0io 0pf+0w