Tue Oct 11 02:29:27 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 02:29:27 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6628929 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 0.6628929 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2530 net assigned charge : 4.500028 assigned positive charge : 408.3275 centred at (gu) : 91.19433 90.66944 90.26543 assigned negative charge : -403.8284 centred at (gu) : 90.99741 90.84424 90.33440 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7922 nv = 96 ne = 84 npr = 54504 no. pairs analyzed = 54504 no. exposed pairs = 3254 no. arc points = 22371 no. surface atoms = 1090 nbur = 1575 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 456 mr = 4550 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.2000000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2058 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9252 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5884960E-08 -3.4135355E-09 midg,1,midg; midg,igrid,midg 4.3656254E-08 -3.1505770E-08 1,midg,midg; igrid,midg,midg -2.4999700E-08 7.0541589E-08 gauss-seidel spectral radius is 0.9882103 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 02:29:28 rms-change max change #iterations 0.1776637 22.10785 at 10iterations 1.8721914E-02 2.448498 at 20iterations 2.0336658E-03 0.2907639 at 30iterations 2.1989147E-04 3.0235052E-02 at 40iterations 2.4149458E-05 3.0746460E-03 at 50iterations finished qdiffx linear iterations at : 02:29:30 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.4149458E-05 3.0746460E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 02:29:31 3.345u 0.176s 0:03.94 89.0% 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 Tue Oct 11 2011 at 02:29:31 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.988679 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 1.988679 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2530 net assigned charge : 4.500028 assigned positive charge : 408.3275 centred at (gu) : 93.58193 92.00766 90.79545 assigned negative charge : -403.8284 centred at (gu) : 92.99197 92.53247 91.00265 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22371 grid for indexing accessible points = 1.400000 m= 31900 mr = 61053 m= 5429 mr = 24068 m= 399 mr = 3592 m= 8 mr = 176 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4227 time to turn everything in is 0.4100000 number of dielectric boundary points 34536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 19973 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) : 0.6628929 object centre at (A) : 43.80500 41.31600 6.319500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3117338E-03 -3.6190111E-02 midg,1,midg; midg,igrid,midg 8.2175791E-02 -1.7401408E-02 1,midg,midg; igrid,midg,midg -1.8845180E-02 5.4429077E-02 gauss-seidel spectral radius is 0.9987512 estimated iterations to convergence 224 setup time was (sec) 0.6200000 now iterating at: 02:29:32 rms-change max change #iterations 4.736369 191.0895 at 10iterations 2.294469 85.63177 at 20iterations 1.107452 35.28374 at 30iterations 0.5370210 16.41212 at 40iterations 0.2601438 7.627964 at 50iterations 0.1257483 4.023298 at 60iterations 6.1074365E-02 1.877424 at 70iterations 2.9559141E-02 0.8815680 at 80iterations 1.4266270E-02 0.4385376 at 90iterations 6.9343159E-03 0.1910477 at 100iterations 3.3608528E-03 9.2117310E-02 at 110iterations 1.6314599E-03 4.7451973E-02 at 120iterations finished qdiffx linear iterations at : 02:29:39 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.6314599E-03 4.7451973E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 02:29:39 7.801u 0.205s 0:08.39 95.3% 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 02:29:40 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2665 !!! WARNING: FMN 398 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.983018 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): 20.39900 67.21100 ymin,ymax (A): 14.46400 68.16800 zmin,zma (A): -17.36000 29.99900 x,y,z range (A): 46.81200 53.70400 47.35900 scale (grids/A): 2.983018 object centre (A): 43.80500 41.31600 6.319500 number of atom coordinates read : 2665 total number of charged atoms : 2530 net assigned charge : 4.500028 assigned positive charge : 408.3275 centred at (gu) : 95.37273 93.01136 91.19290 assigned negative charge : -403.8284 centred at (gu) : 94.48794 93.79864 91.50388 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22371 grid for indexing accessible points = 1.400000 m= 102587 mr = 147538 m= 38450 mr = 85038 m= 10119 mr = 31538 m= 1678 mr = 7917 m= 120 mr = 1154 m= 0 mr = 62 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 14036 time to turn everything in is 1.070000 number of dielectric boundary points 77993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20240 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) : 1.988679 object centre at (A) : 43.80500 41.31600 6.319500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1517006 -0.3933789 midg,1,midg; midg,igrid,midg 1.046819 -0.3821062 1,midg,midg; igrid,midg,midg -0.1890876 0.4333958 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 1.300000 now iterating at: 02:29:41 rms-change max change #iterations 10.83588 448.0103 at 10iterations 6.328780 155.7670 at 20iterations 3.700112 66.42564 at 30iterations 2.162196 35.89807 at 40iterations 1.259058 22.46840 at 50iterations 0.7315502 13.45727 at 60iterations 0.4259872 7.676150 at 70iterations 0.2477180 4.584150 at 80iterations 0.1439573 2.489293 at 90iterations 8.3564825E-02 1.407162 at 100iterations 4.8593152E-02 0.7894173 at 110iterations 2.8220601E-02 0.4821625 at 120iterations 1.6346369E-02 0.2848053 at 130iterations 9.4890017E-03 0.1677628 at 140iterations 5.5091702E-03 8.7768555E-02 at 150iterations 3.1932425E-03 5.2999496E-02 at 160iterations 1.8562389E-03 3.1740904E-02 at 170iterations 1.0757120E-03 1.7705917E-02 at 180iterations finished qdiffx linear iterations at : 02:29:52 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 1.0757120E-03 1.7705917E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 02:29:53 12.798u 0.228s 0:13.40 97.0% 0+0k 0+0io 0pf+0w