Mon Oct 10 17:02:53 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 Mon Oct 10 2011 at 17:02:53 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5909891 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 0.5909891 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.485970 assigned positive charge : 423.4342 centred at (gu) : 89.19022 89.77065 89.21916 assigned negative charge : -425.9213 centred at (gu) : 89.18981 89.59818 89.06170 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6470 nv = 96 ne = 84 npr = 55943 no. pairs analyzed = 55943 no. exposed pairs = 3760 no. arc points = 26448 no. surface atoms = 1269 nbur = 1521 mkacc time = 0.1200000 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= 297 mr = 3230 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6726997E-09 3.2706533E-09 midg,1,midg; midg,igrid,midg -6.3595311E-09 4.1358921E-09 1,midg,midg; igrid,midg,midg -8.8444774E-10 -5.9692412E-10 gauss-seidel spectral radius is 0.9852079 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 17:02:55 rms-change max change #iterations 0.1052420 15.91405 at 10iterations 8.4811980E-03 1.428350 at 20iterations 6.9692958E-04 0.1110249 at 30iterations 5.7195481E-05 8.9778900E-03 at 40iterations 4.7068293E-06 6.5994263E-04 at 50iterations finished qdiffx linear iterations at : 17:02:57 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 4.7068293E-06 6.5994263E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 17:02:58 3.150u 0.151s 0:05.43 60.7% 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 17:02:58 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.772967 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 1.772967 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.485970 assigned positive charge : 423.4342 centred at (gu) : 87.57001 89.31070 87.65668 assigned negative charge : -425.9213 centred at (gu) : 87.56922 88.79423 87.18475 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26448 grid for indexing accessible points = 1.400000 m= 22590 mr = 46448 m= 2759 mr = 15426 m= 91 mr = 1441 m= 0 mr = 16 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 173 time to turn everything in is 0.4900000 number of dielectric boundary points 32409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20655 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) : 0.5909891 object centre at (A) : 18.70900 -4.518000 -17.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4074875E-02 8.4068887E-03 midg,1,midg; midg,igrid,midg -1.0740043E-02 4.9444363E-03 1,midg,midg; igrid,midg,midg 6.0573644E-03 -1.3703898E-03 gauss-seidel spectral radius is 0.9984531 estimated iterations to convergence 202 setup time was (sec) 0.7600000 now iterating at: 17:02:59 rms-change max change #iterations 3.924914 207.0208 at 10iterations 1.740517 68.98889 at 20iterations 0.7770067 26.43784 at 30iterations 0.3460396 11.94897 at 40iterations 0.1548658 5.287850 at 50iterations 6.8967596E-02 2.211483 at 60iterations 3.0802188E-02 0.9792889 at 70iterations 1.3738669E-02 0.4693298 at 80iterations 6.1198086E-03 0.2181797 at 90iterations 2.7332455E-03 8.8760376E-02 at 100iterations 1.2193526E-03 3.9367676E-02 at 110iterations 5.4332882E-04 1.8530369E-02 at 120iterations finished qdiffx linear iterations at : 17:03:05 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 5.4332882E-04 1.8530369E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 17:03:06 7.075u 0.153s 0:07.51 96.1% 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 17:03:06 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2790 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.659451 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): -11.41000 48.82800 ymin,ymax (A): -26.27500 17.23900 zmin,zma (A): -41.69800 5.890000 x,y,z range (A): 60.23800 43.51400 47.58800 scale (grids/A): 2.659451 object centre (A): 18.70900 -4.518000 -17.90400 number of atom coordinates read : 2790 total number of charged atoms : 2649 net assigned charge : -2.485970 assigned positive charge : 423.4342 centred at (gu) : 86.35485 88.96615 86.48484 assigned negative charge : -425.9213 centred at (gu) : 86.35378 88.19122 85.77705 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 162933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26448 grid for indexing accessible points = 1.400000 m= 75789 mr = 113540 m= 23514 mr = 59404 m= 4541 mr = 17740 m= 398 mr = 3074 m= 5 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 1.210000 number of dielectric boundary points 73218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21186 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) : 1.772967 object centre at (A) : 18.70900 -4.518000 -17.90400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2693557 0.1274704 midg,1,midg; midg,igrid,midg -9.4167225E-02 3.9556529E-02 1,midg,midg; igrid,midg,midg 0.1347575 0.3326544 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 1.480000 now iterating at: 17:03:07 rms-change max change #iterations 9.672880 336.7054 at 10iterations 5.654050 148.2115 at 20iterations 3.259957 81.11195 at 30iterations 1.874956 42.22408 at 40iterations 1.074081 22.92880 at 50iterations 0.6136714 12.96166 at 60iterations 0.3499514 8.266047 at 70iterations 0.1994196 4.762637 at 80iterations 0.1136349 2.469833 at 90iterations 6.4556919E-02 1.196136 at 100iterations 3.6654387E-02 0.7031479 at 110iterations 2.0797977E-02 0.4287376 at 120iterations 1.1845670E-02 0.2221642 at 130iterations 6.7181322E-03 0.1459227 at 140iterations 3.8122903E-03 7.2673798E-02 at 150iterations 2.1676142E-03 4.0143967E-02 at 160iterations 1.2282057E-03 2.5253296E-02 at 170iterations 6.9660775E-04 1.3405085E-02 at 180iterations finished qdiffx linear iterations at : 17:03:17 total time elapsed so far: 11.00000 # loops : 180 mean,max change (kT/e) : 6.9660775E-04 1.3405085E-02 energy calculations done at 11.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 17:03:17 11.187u 0.184s 0:11.73 96.8% 0+0k 0+0io 0pf+0w