Sat Oct 15 13:43:26 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 15 2011 at 13:43:26 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 = 3402 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: 0.4817647 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 0.4817647 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.99998 assigned positive charge : 517.4219 centred at (gu) : 88.71573 88.91412 88.59634 assigned negative charge : -535.4238 centred at (gu) : 88.77853 88.85420 88.59696 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5147 nv = 96 ne = 84 npr = 63491 no. pairs analyzed = 63491 no. exposed pairs = 5068 no. arc points = 36708 no. surface atoms = 1672 nbur = 1730 mkacc time = 0.1100000 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 = 1.764000 m= 176 mr = 2183 m= 0 mr = 3 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3437 ## 634 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 6965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5004553E-11 -4.4893311E-11 midg,1,midg; midg,igrid,midg -1.3057555E-10 -2.5688673E-11 1,midg,midg; igrid,midg,midg -4.5465371E-11 -6.9257607E-11 gauss-seidel spectral radius is 0.9779100 estimated iterations to convergence 56 setup time was (sec) 0.4300000 now iterating at: 13:43:27 rms-change max change #iterations 4.0913656E-02 9.527496 at 10iterations 2.3023332E-03 0.4614372 at 20iterations 3.1799782E-04 9.5745087E-02 at 30iterations 7.2925221E-05 2.3044586E-02 at 40iterations 1.7328304E-05 5.5866241E-03 at 50iterations finished qdiffx linear iterations at : 13:43:32 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.7328304E-05 5.5866241E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 13:43:33 3.584u 0.199s 0:06.95 54.2% 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 Sat Oct 15 2011 at 13:43:33 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 = 3402 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: 1.445294 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 1.445294 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.99998 assigned positive charge : 517.4219 centred at (gu) : 86.14629 86.74142 85.78779 assigned negative charge : -535.4238 centred at (gu) : 86.33517 86.56247 85.79028 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 57853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 13907 mr = 34878 m= 956 mr = 7910 m= 9 mr = 278 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.3000000 number of dielectric boundary points 29659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 570 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 23849 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) : 0.4817647 object centre at (A) : -0.9190006 -27.04400 -49.59450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1924917E-03 -1.0715969E-02 midg,1,midg; midg,igrid,midg -1.0750321E-02 -2.9075434E-03 1,midg,midg; igrid,midg,midg -8.3807175E-04 -6.1497334E-03 gauss-seidel spectral radius is 0.9977219 estimated iterations to convergence 167 setup time was (sec) 0.5300000 now iterating at: 13:43:34 rms-change max change #iterations 2.745873 139.0523 at 10iterations 1.028232 54.22169 at 20iterations 0.3829091 16.91020 at 30iterations 0.1428545 5.821167 at 40iterations 5.3832274E-02 2.164610 at 50iterations 2.0080527E-02 0.8488026 at 60iterations 7.6361438E-03 0.3172398 at 70iterations 2.9311569E-03 0.1268749 at 80iterations 1.1597275E-03 5.7113647E-02 at 90iterations 4.9026520E-04 2.6242256E-02 at 100iterations 2.3022838E-04 1.3127327E-02 at 110iterations 1.2054892E-04 7.4501038E-03 at 120iterations finished qdiffx linear iterations at : 13:43:43 total time elapsed so far: 8.110000 # loops : 120 mean,max change (kT/e) : 1.2054892E-04 7.4501038E-03 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 13:43:43 8.250u 0.237s 0:09.96 85.1% 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 15 2011 at 13:43:43 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 = 3402 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: 2.167941 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): -28.07900 26.24100 ymin,ymax (A): -55.20700 1.119000 zmin,zma (A): -86.54200 -12.64700 x,y,z range (A): 54.32000 56.32600 73.89500 scale (grids/A): 2.167941 object centre (A): -0.9190006 -27.04400 -49.59450 number of atom coordinates read : 3402 total number of charged atoms : 3237 net assigned charge : -17.99998 assigned positive charge : 517.4219 centred at (gu) : 84.21918 85.11160 83.68140 assigned negative charge : -535.4238 centred at (gu) : 84.50276 84.84352 83.68531 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 135049 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36708 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 51625 mr = 87477 m= 10926 mr = 36728 m= 1193 mr = 6939 m= 39 mr = 593 m= 0 mr = 4 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 276 time to turn everything in is 0.7000000 number of dielectric boundary points 67091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25760 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) : 1.445294 object centre at (A) : -0.9190006 -27.04400 -49.59450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9834660E-02 -0.2720737 midg,1,midg; midg,igrid,midg -0.1946288 -5.3807203E-02 1,midg,midg; igrid,midg,midg 5.3526014E-03 -0.1240782 gauss-seidel spectral radius is 0.9989942 estimated iterations to convergence 249 setup time was (sec) 0.9400000 now iterating at: 13:43:44 rms-change max change #iterations 7.819561 306.8049 at 10iterations 4.217578 128.1653 at 20iterations 2.257082 64.86659 at 30iterations 1.202601 35.44055 at 40iterations 0.6395009 17.48918 at 50iterations 0.3366675 9.743079 at 60iterations 0.1779244 4.403332 at 70iterations 9.3876630E-02 2.365410 at 80iterations 4.9440607E-02 1.163795 at 90iterations 2.6002275E-02 0.5839654 at 100iterations 1.3597445E-02 0.3308315 at 110iterations 7.1300282E-03 0.1938400 at 120iterations 3.7492660E-03 8.5019112E-02 at 130iterations 1.9727389E-03 4.7035217E-02 at 140iterations 1.0377393E-03 2.8305054E-02 at 150iterations 5.4949801E-04 1.3694763E-02 at 160iterations 2.9321376E-04 7.9269409E-03 at 170iterations 1.5904827E-04 4.1570663E-03 at 180iterations finished qdiffx linear iterations at : 13:43:56 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.5904827E-04 4.1570663E-03 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 13:43:57 12.916u 0.221s 0:13.49 97.3% 0+0k 0+0io 0pf+0w