Tue Oct 11 06:36:28 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 06:36:28 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 = 2073 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: 0.7047412 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 0.7047412 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 90.08955 90.29941 89.42870 assigned negative charge : -306.8872 centred at (gu) : 89.90961 90.27463 89.40302 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6955 nv = 96 ne = 84 npr = 41824 no. pairs analyzed = 41824 no. exposed pairs = 2485 no. arc points = 16892 no. surface atoms = 843 nbur = 1230 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4031 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2945129E-08 6.3802709E-08 midg,1,midg; midg,igrid,midg 4.5419565E-08 7.4864694E-08 1,midg,midg; igrid,midg,midg -2.4008175E-08 1.4278785E-07 gauss-seidel spectral radius is 0.9895025 estimated iterations to convergence 79 setup time was (sec) 0.4600000 now iterating at: 06:36:29 rms-change max change #iterations 0.1969750 30.43214 at 10iterations 2.4289422E-02 3.412681 at 20iterations 3.1391999E-03 0.4405403 at 30iterations 4.7556046E-04 6.5162659E-02 at 40iterations 1.0570335E-04 1.4997482E-02 at 50iterations finished qdiffx linear iterations at : 06:36:31 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.0570335E-04 1.4997482E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 06:36:31 3.108u 0.148s 0:03.54 91.5% 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 Tue Oct 11 2011 at 06:36:32 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 = 2073 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: 2.114223 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 2.114223 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 90.26848 90.89791 88.28569 assigned negative charge : -306.8872 centred at (gu) : 89.72892 90.82392 88.20924 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16892 grid for indexing accessible points = 1.400000 m= 29409 mr = 53111 m= 5725 mr = 22334 m= 505 mr = 3811 m= 14 mr = 260 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15450 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) : 0.7047412 object centre at (A) : 1.942000 -8.077000 11.36750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8554543E-02 4.4076230E-02 midg,1,midg; midg,igrid,midg 7.2153462E-03 3.2596763E-02 1,midg,midg; igrid,midg,midg 8.5443603E-03 4.1463055E-02 gauss-seidel spectral radius is 0.9988213 estimated iterations to convergence 231 setup time was (sec) 0.8200000 now iterating at: 06:36:32 rms-change max change #iterations 4.546133 174.7922 at 10iterations 2.242096 79.13003 at 20iterations 1.109933 33.52753 at 30iterations 0.5509340 17.78592 at 40iterations 0.2732611 7.879707 at 50iterations 0.1348674 4.229778 at 60iterations 6.6735104E-02 2.083622 at 70iterations 3.3194005E-02 1.023201 at 80iterations 1.6435148E-02 0.4803810 at 90iterations 8.1787892E-03 0.2640762 at 100iterations 4.0709754E-03 0.1233521 at 110iterations 2.0328811E-03 6.3568115E-02 at 120iterations finished qdiffx linear iterations at : 06:36:39 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.0328811E-03 6.3568115E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 06:36:39 7.063u 0.192s 0:07.85 92.3% 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 06:36:39 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.171335 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): -20.02900 23.91300 ymin,ymax (A): -28.45900 12.30500 zmin,zma (A): -13.89000 36.62500 x,y,z range (A): 43.94200 40.76400 50.51500 scale (grids/A): 3.171335 object centre (A): 1.942000 -8.077000 11.36750 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 7.500009 assigned positive charge : 314.3870 centred at (gu) : 90.40284 91.34696 87.42851 assigned negative charge : -306.8872 centred at (gu) : 89.59349 91.23591 87.31387 start vw surface at 0.1400000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 171163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16892 grid for indexing accessible points = 1.400000 m= 92550 mr = 127803 m= 37042 mr = 77073 m= 10663 mr = 30461 m= 2085 mr = 8254 m= 229 mr = 1520 m= 7 mr = 155 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 68471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 15560 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) : 2.114223 object centre at (A) : 1.942000 -8.077000 11.36750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6233775 0.3758006 midg,1,midg; midg,igrid,midg 3.1480372E-02 0.2503471 1,midg,midg; igrid,midg,midg 0.1759633 0.3336428 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.980000 now iterating at: 06:36:42 rms-change max change #iterations 10.10612 346.8717 at 10iterations 5.961987 126.5438 at 20iterations 3.508176 76.05635 at 30iterations 2.064881 39.37857 at 40iterations 1.209552 26.18051 at 50iterations 0.7102313 15.43348 at 60iterations 0.4157330 7.676742 at 70iterations 0.2429411 4.378571 at 80iterations 0.1424311 2.827421 at 90iterations 8.3285183E-02 1.677330 at 100iterations 4.8718635E-02 0.9514227 at 110iterations 2.8632227E-02 0.5043011 at 120iterations 1.6861038E-02 0.3639126 at 130iterations 1.0036169E-02 0.1991806 at 140iterations 6.1007673E-03 0.1165142 at 150iterations 3.7945779E-03 7.8514099E-02 at 160iterations 2.4849984E-03 4.6142578E-02 at 170iterations 1.7101372E-03 3.0509949E-02 at 180iterations finished qdiffx linear iterations at : 06:36:51 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 1.7101372E-03 3.0509949E-02 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 06:36:52 11.710u 0.187s 0:12.37 96.1% 0+0k 0+0io 0pf+0w