Sun Oct 9 22:07:37 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 Sun Oct 9 2011 at 22:07:37 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 0.5792479 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): -1.191000 55.45700 ymin,ymax (A): -24.07600 37.38300 zmin,zma (A): -8.294000 47.10600 x,y,z range (A): 56.64800 61.45900 55.40000 scale (grids/A): 0.5792479 object centre (A): 27.13300 6.653502 19.40600 number of atom coordinates read : 3203 total number of charged atoms : 3052 net assigned charge : 4.025013 assigned positive charge : 487.0996 centred at (gu) : 89.81577 90.80848 90.42133 assigned negative charge : -483.0760 centred at (gu) : 89.78433 90.92385 90.41040 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7005 nv = 96 ne = 84 npr = 63203 no. pairs analyzed = 63203 no. exposed pairs = 4098 no. arc points = 29398 no. surface atoms = 1375 nbur = 1828 mkacc time = 0.1400000 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= 321 mr = 3569 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2998 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7160426E-10 1.2532864E-09 midg,1,midg; midg,igrid,midg 2.9259548E-09 -2.2510924E-09 1,midg,midg; igrid,midg,midg 1.5136356E-10 1.5458522E-09 gauss-seidel spectral radius is 0.9846411 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 22:07:38 rms-change max change #iterations 0.1033230 15.56094 at 10iterations 7.8651020E-03 1.295866 at 20iterations 6.2578806E-04 9.2851639E-02 at 30iterations 5.0273789E-05 7.6627731E-03 at 40iterations 4.8793872E-06 6.5708160E-04 at 50iterations finished qdiffx linear iterations at : 22:07:40 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 4.8793872E-06 6.5708160E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 22:07:41 3.123u 0.147s 0:03.54 92.0% 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 Sun Oct 9 2011 at 22:07:41 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 1.737744 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): -1.191000 55.45700 ymin,ymax (A): -24.07600 37.38300 zmin,zma (A): -8.294000 47.10600 x,y,z range (A): 56.64800 61.45900 55.40000 scale (grids/A): 1.737744 object centre (A): 27.13300 6.653502 19.40600 number of atom coordinates read : 3203 total number of charged atoms : 3052 net assigned charge : 4.025013 assigned positive charge : 487.0996 centred at (gu) : 89.44635 92.42432 91.26273 assigned negative charge : -483.0760 centred at (gu) : 89.35267 92.77126 91.23087 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29398 grid for indexing accessible points = 1.400000 m= 24556 mr = 52255 m= 3023 mr = 16868 m= 121 mr = 1533 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 760 time to turn everything in is 0.5200000 number of dielectric boundary points 34711 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 293 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23671 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) : 0.5792479 object centre at (A) : 27.13300 6.653502 19.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3497593E-03 7.8620575E-03 midg,1,midg; midg,igrid,midg -4.8941020E-03 -1.4584504E-02 1,midg,midg; igrid,midg,midg 7.7469060E-03 -2.3612469E-03 gauss-seidel spectral radius is 0.9984387 estimated iterations to convergence 201 setup time was (sec) 0.8200000 now iterating at: 22:07:42 rms-change max change #iterations 3.968751 160.3822 at 10iterations 1.749446 60.08493 at 20iterations 0.7769901 26.38722 at 30iterations 0.3434769 11.27707 at 40iterations 0.1524886 5.456482 at 50iterations 6.7590840E-02 2.416214 at 60iterations 3.0091876E-02 1.011757 at 70iterations 1.3390018E-02 0.5058594 at 80iterations 5.9211086E-03 0.2009630 at 90iterations 2.6293162E-03 8.3892822E-02 at 100iterations 1.1698869E-03 3.8515091E-02 at 110iterations 5.1979028E-04 1.7517090E-02 at 120iterations finished qdiffx linear iterations at : 22:07:48 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 5.1979028E-04 1.7517090E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 22:07:48 7.112u 0.187s 0:07.59 96.0% 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 Sun Oct 9 2011 at 22:07:48 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 139 has a net charge of -0.4750 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: 2.606616 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): -1.191000 55.45700 ymin,ymax (A): -24.07600 37.38300 zmin,zma (A): -8.294000 47.10600 x,y,z range (A): 56.64800 61.45900 55.40000 scale (grids/A): 2.606616 object centre (A): 27.13300 6.653502 19.40600 number of atom coordinates read : 3203 total number of charged atoms : 3052 net assigned charge : 4.025013 assigned positive charge : 487.0996 centred at (gu) : 89.16904 93.63650 91.89400 assigned negative charge : -483.0760 centred at (gu) : 89.02889 94.15691 91.84615 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 179930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29398 grid for indexing accessible points = 1.400000 m= 83123 mr = 127519 m= 25355 mr = 65644 m= 4909 mr = 18808 m= 519 mr = 3354 m= 16 mr = 293 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 2580 time to turn everything in is 1.280000 number of dielectric boundary points 78234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 24401 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) : 1.737744 object centre at (A) : 27.13300 6.653502 19.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9933337E-02 9.0650991E-02 midg,1,midg; midg,igrid,midg -0.3236081 -0.3700420 1,midg,midg; igrid,midg,midg 7.5871103E-02 -7.0762545E-02 gauss-seidel spectral radius is 0.9992221 estimated iterations to convergence 283 setup time was (sec) 1.560000 now iterating at: 22:07:50 rms-change max change #iterations 9.880307 317.0564 at 10iterations 5.766168 145.3563 at 20iterations 3.321570 79.83333 at 30iterations 1.908576 47.73156 at 40iterations 1.093240 26.42584 at 50iterations 0.6251189 13.79252 at 60iterations 0.3561496 7.645411 at 70iterations 0.2027799 4.041142 at 80iterations 0.1154175 2.184600 at 90iterations 6.5692455E-02 1.264978 at 100iterations 3.7276074E-02 0.7481647 at 110iterations 2.1128457E-02 0.3913364 at 120iterations 1.2020760E-02 0.2204862 at 130iterations 6.8214252E-03 0.1375847 at 140iterations 3.8605703E-03 7.4606419E-02 at 150iterations 2.1877582E-03 3.8436890E-02 at 160iterations 1.2427066E-03 2.2804260E-02 at 170iterations 7.0362980E-04 1.2741089E-02 at 180iterations finished qdiffx linear iterations at : 22:08:00 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 7.0362980E-04 1.2741089E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 22:08:00 11.245u 0.167s 0:11.69 97.5% 0+0k 0+0io 0pf+0w