Mon Oct 10 17:00:49 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 17:00:49 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 = 3286 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: 0.6489245 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): 13.23000 62.60400 ymin,ymax (A): -41.12700 10.45300 zmin,zma (A): 31.46100 86.32100 x,y,z range (A): 49.37400 51.58000 54.86000 scale (grids/A): 0.6489245 object centre (A): 37.91700 -15.33700 58.89100 number of atom coordinates read : 3286 total number of charged atoms : 3138 net assigned charge : 4.000038 assigned positive charge : 500.4807 centred at (gu) : 89.20625 91.21718 89.44604 assigned negative charge : -496.4816 centred at (gu) : 89.25977 91.21077 89.50838 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9110 nv = 96 ne = 84 npr = 66930 no. pairs analyzed = 66930 no. exposed pairs = 3799 no. arc points = 26159 no. surface atoms = 1286 nbur = 2000 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 5370 m= 0 mr = 83 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2500000 number of dielectric boundary points 4190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2522 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 11070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1396552E-08 -4.0167500E-09 midg,1,midg; midg,igrid,midg 4.7783391E-09 1.0956655E-08 1,midg,midg; igrid,midg,midg 2.0556332E-08 -2.3712103E-09 gauss-seidel spectral radius is 0.9877459 estimated iterations to convergence 74 setup time was (sec) 0.4500000 now iterating at: 17:00:49 rms-change max change #iterations 0.1807788 24.59315 at 10iterations 1.8931644E-02 2.100376 at 20iterations 2.6369423E-03 0.3239098 at 30iterations 9.3576644E-04 0.1125145 at 40iterations 4.6371031E-04 5.2032471E-02 at 50iterations finished qdiffx linear iterations at : 17:00:52 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.6371031E-04 5.2032471E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 17:00:53 3.459u 0.171s 0:04.31 83.9% 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 17:00:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 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: 1.946774 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): 13.23000 62.60400 ymin,ymax (A): -41.12700 10.45300 zmin,zma (A): 31.46100 86.32100 x,y,z range (A): 49.37400 51.58000 54.86000 scale (grids/A): 1.946774 object centre (A): 37.91700 -15.33700 58.89100 number of atom coordinates read : 3286 total number of charged atoms : 3138 net assigned charge : 4.000038 assigned positive charge : 500.4807 centred at (gu) : 87.61803 93.65051 88.33731 assigned negative charge : -496.4816 centred at (gu) : 87.77872 93.63185 88.52456 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 98362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26159 grid for indexing accessible points = 1.400000 m= 37921 mr = 71109 m= 6592 mr = 28777 m= 540 mr = 4410 m= 15 mr = 261 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 756 time to turn everything in is 0.4800000 number of dielectric boundary points 38871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 24727 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) : 0.6489245 object centre at (A) : 37.91700 -15.33700 58.89100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2710042E-02 3.9249798E-03 midg,1,midg; midg,igrid,midg 2.8396607E-03 2.7360028E-02 1,midg,midg; igrid,midg,midg 2.1463688E-02 3.7845273E-02 gauss-seidel spectral radius is 0.9987472 estimated iterations to convergence 224 setup time was (sec) 0.7000000 now iterating at: 17:00:54 rms-change max change #iterations 5.052512 184.7211 at 10iterations 2.447204 71.69033 at 20iterations 1.191421 31.33550 at 30iterations 0.5787296 16.45413 at 40iterations 0.2810363 7.967250 at 50iterations 0.1366016 3.980659 at 60iterations 6.6097729E-02 1.814787 at 70iterations 3.2138616E-02 0.8847185 at 80iterations 1.5692754E-02 0.4374905 at 90iterations 7.7259699E-03 0.2067289 at 100iterations 3.9180759E-03 0.1126251 at 110iterations 2.0748931E-03 5.7991028E-02 at 120iterations finished qdiffx linear iterations at : 17:01:01 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.0748931E-03 5.7991028E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 17:01:02 7.987u 0.212s 0:09.17 89.3% 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 Mon Oct 10 2011 at 17:01:02 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 = 3286 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: 2.920160 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): 13.23000 62.60400 ymin,ymax (A): -41.12700 10.45300 zmin,zma (A): 31.46100 86.32100 x,y,z range (A): 49.37400 51.58000 54.86000 scale (grids/A): 2.920160 object centre (A): 37.91700 -15.33700 58.89100 number of atom coordinates read : 3286 total number of charged atoms : 3138 net assigned charge : 4.000038 assigned positive charge : 500.4807 centred at (gu) : 86.42668 95.47565 87.50563 assigned negative charge : -496.4816 centred at (gu) : 86.66788 95.44794 87.78671 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 227186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26159 grid for indexing accessible points = 1.400000 m= 120999 mr = 171324 m= 46119 mr = 100944 m= 12279 mr = 37770 m= 2200 mr = 9626 m= 197 mr = 1588 m= 8 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 2435 time to turn everything in is 1.280000 number of dielectric boundary points 87638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 25104 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) : 1.946774 object centre at (A) : 37.91700 -15.33700 58.89100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3330481 0.2647319 midg,1,midg; midg,igrid,midg -2.7353389E-02 0.3878682 1,midg,midg; igrid,midg,midg 0.1670922 0.4902761 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 1.520000 now iterating at: 17:01:04 rms-change max change #iterations 11.82450 315.4094 at 10iterations 7.089568 186.0034 at 20iterations 4.233598 83.64529 at 30iterations 2.520408 48.12719 at 40iterations 1.492820 27.42802 at 50iterations 0.8794820 16.78330 at 60iterations 0.5188984 9.159678 at 70iterations 0.3057795 4.954155 at 80iterations 0.1799001 2.933897 at 90iterations 0.1055574 1.727116 at 100iterations 6.2110934E-02 0.9984436 at 110iterations 3.6323380E-02 0.6075134 at 120iterations 2.1315726E-02 0.3521118 at 130iterations 1.2506962E-02 0.1917796 at 140iterations 7.3096645E-03 0.1104269 at 150iterations 4.2910171E-03 6.7001343E-02 at 160iterations 2.5174420E-03 4.0990829E-02 at 170iterations 1.4860595E-03 2.2817612E-02 at 180iterations finished qdiffx linear iterations at : 17:01:16 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 1.4860595E-03 2.2817612E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 17:01:16 13.422u 0.215s 0:14.11 96.5% 0+0k 0+0io 0pf+0w