Mon Oct 10 14:01:01 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 Mon Oct 10 2011 at 14:01:01 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 = 2095 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: 0.6126418 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 0.6126418 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.499998 assigned positive charge : 274.9211 centred at (gu) : 91.89372 90.13938 90.83065 assigned negative charge : -277.4213 centred at (gu) : 91.81159 90.15894 91.13101 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5505 nv = 96 ne = 84 npr = 44097 no. pairs analyzed = 44097 no. exposed pairs = 2843 no. arc points = 20539 no. surface atoms = 971 nbur = 1124 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2671 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1856 ## 102 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8869711E-09 -1.6150794E-08 midg,1,midg; midg,igrid,midg -7.6849005E-10 -2.3508508E-09 1,midg,midg; igrid,midg,midg -3.0901686E-09 2.4734004E-09 gauss-seidel spectral radius is 0.9861780 estimated iterations to convergence 70 setup time was (sec) 0.6800000 now iterating at: 14:01:02 rms-change max change #iterations 9.8501086E-02 15.58636 at 10iterations 9.0554394E-03 1.680742 at 20iterations 8.3520450E-04 0.1283164 at 30iterations 1.1377532E-04 2.0530701E-02 at 40iterations 2.5003243E-05 4.3163300E-03 at 50iterations finished qdiffx linear iterations at : 14:01:08 total time elapsed so far: 6.480000 # loops : 50 mean,max change (kT/e) : 2.5003243E-05 4.3163300E-03 energy calculations done at 6.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.670000 DelPhi exited at 14:01:09 6.674u 0.614s 0:07.90 92.1% 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 Mon Oct 10 2011 at 14:01:10 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 = 2095 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: 1.837925 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 1.837925 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.499998 assigned positive charge : 274.9211 centred at (gu) : 95.68117 90.41838 92.49207 assigned negative charge : -277.4213 centred at (gu) : 95.43510 90.47690 93.39309 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20539 grid for indexing accessible points = 1.400000 m= 19764 mr = 38762 m= 2958 mr = 13337 m= 157 mr = 1579 m= 0 mr = 41 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 28625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15430 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) : 0.6126418 object centre at (A) : 11.97150 28.56150 63.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2367717E-02 -6.7074761E-02 midg,1,midg; midg,igrid,midg 3.5564534E-03 1.8552600E-03 1,midg,midg; igrid,midg,midg -6.2262299E-03 -5.2282115E-04 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 0.9400000 now iterating at: 14:01:11 rms-change max change #iterations 3.301953 182.9190 at 10iterations 1.487594 92.12569 at 20iterations 0.6734118 27.09829 at 30iterations 0.3046267 11.63533 at 40iterations 0.1381629 5.670540 at 50iterations 6.2478814E-02 2.303947 at 60iterations 2.8246356E-02 1.059774 at 70iterations 1.2849916E-02 0.4860377 at 80iterations 5.7913903E-03 0.2001190 at 90iterations 2.6320224E-03 0.1118526 at 100iterations 1.1900828E-03 4.2837143E-02 at 110iterations 5.4090458E-04 2.0806551E-02 at 120iterations finished qdiffx linear iterations at : 14:01:26 total time elapsed so far: 16.04000 # loops : 120 mean,max change (kT/e) : 5.4090458E-04 2.0806551E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 14:01:27 16.214u 0.686s 0:17.55 96.2% 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 Mon Oct 10 2011 at 14:01:27 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 = 2095 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: 2.756888 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 2.756888 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.499998 assigned positive charge : 274.9211 centred at (gu) : 98.52175 90.62755 93.73805 assigned negative charge : -277.4213 centred at (gu) : 98.15276 90.71552 95.08971 start vw surface at 0.1300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 137427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20539 grid for indexing accessible points = 1.400000 m= 63863 mr = 94505 m= 22414 mr = 49715 m= 5087 mr = 16860 m= 621 mr = 3433 m= 26 mr = 368 m= 0 mr = 8 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 64549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 15700 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) : 1.837925 object centre at (A) : 11.97150 28.56150 63.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3189013 -0.7565358 midg,1,midg; midg,igrid,midg 2.9671680E-02 1.6036788E-02 1,midg,midg; igrid,midg,midg -4.8101556E-02 -1.3977814E-02 gauss-seidel spectral radius is 0.9992259 estimated iterations to convergence 284 setup time was (sec) 1.950000 now iterating at: 14:01:30 rms-change max change #iterations 7.925478 308.5873 at 10iterations 4.610919 129.4568 at 20iterations 2.644984 69.95303 at 30iterations 1.517511 34.01801 at 40iterations 0.8672453 21.75846 at 50iterations 0.4964455 11.13787 at 60iterations 0.2821825 5.866866 at 70iterations 0.1610324 3.621824 at 80iterations 9.1417432E-02 1.916608 at 90iterations 5.2052755E-02 1.067015 at 100iterations 2.9563684E-02 0.6355839 at 110iterations 1.6811527E-02 0.3536625 at 120iterations 9.5368894E-03 0.2125351 at 130iterations 5.4316968E-03 0.1110802 at 140iterations 3.0965521E-03 6.0507774E-02 at 150iterations 1.7640078E-03 3.4978688E-02 at 160iterations 1.0138003E-03 2.1408081E-02 at 170iterations 5.8674568E-04 1.3270855E-02 at 180iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 26.95000 # loops : 180 mean,max change (kT/e) : 5.8674568E-04 1.3270855E-02 energy calculations done at 26.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.11000 DelPhi exited at 14:01:56 27.116u 0.812s 0:29.05 96.1% 0+0k 0+0io 0pf+0w