Sun Oct 9 08:16:33 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 Sun Oct 9 2011 at 08:16:33 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5210316 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): -22.33700 45.98900 ymin,ymax (A): 4.810000 68.06001 zmin,zma (A): -110.9840 -43.64500 x,y,z range (A): 68.32600 63.25000 67.33900 scale (grids/A): 0.5210316 object centre (A): 11.82600 36.43500 -77.31450 number of atom coordinates read : 5631 total number of charged atoms : 5463 net assigned charge : -0.4999426 assigned positive charge : 847.9505 centred at (gu) : 90.62717 90.76816 89.13578 assigned negative charge : -848.4578 centred at (gu) : 90.65112 90.74686 88.98582 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9736 nv = 96 ne = 84 npr = 113036 no. pairs analyzed = 113036 no. exposed pairs = 7268 no. arc points = 50694 no. surface atoms = 2424 nbur = 3207 mkacc time = 0.2400000 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 = 1.652000 m= 354 mr = 4966 m= 0 mr = 14 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.5200000 number of dielectric boundary points 5110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4937 ## 677 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 13039 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2017438E-10 5.5562427E-10 midg,1,midg; midg,igrid,midg -8.6421710E-11 1.1926628E-10 1,midg,midg; igrid,midg,midg 9.3145262E-11 -1.3945244E-10 gauss-seidel spectral radius is 0.9812247 estimated iterations to convergence 60 setup time was (sec) 0.7300000 now iterating at: 08:16:34 rms-change max change #iterations 8.3993502E-02 13.87551 at 10iterations 5.2452651E-03 0.8276863 at 20iterations 5.0184445E-04 9.0068817E-02 at 30iterations 1.1681906E-04 2.2365570E-02 at 40iterations 3.4737437E-05 6.1511993E-03 at 50iterations finished qdiffx linear iterations at : 08:16:37 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 3.4737437E-05 6.1511993E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:16:37 3.341u 0.133s 0:03.77 92.0% 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 Sun Oct 9 2011 at 08:16:37 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.563095 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): -22.33700 45.98900 ymin,ymax (A): 4.810000 68.06001 zmin,zma (A): -110.9840 -43.64500 x,y,z range (A): 68.32600 63.25000 67.33900 scale (grids/A): 1.563095 object centre (A): 11.82600 36.43500 -77.31450 number of atom coordinates read : 5631 total number of charged atoms : 5463 net assigned charge : -0.4999426 assigned positive charge : 847.9505 centred at (gu) : 91.87975 92.30291 87.40556 assigned negative charge : -848.4578 centred at (gu) : 91.95273 92.24050 86.95736 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 108416 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 32230 mr = 73333 m= 3154 mr = 21675 m= 69 mr = 1421 m= 0 mr = 6 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2810 time to turn everything in is 0.7300000 number of dielectric boundary points 47434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 562 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 41241 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) : 0.5210316 object centre at (A) : 11.82600 36.43500 -77.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4213103E-02 1.9269606E-02 midg,1,midg; midg,igrid,midg -3.5217851E-03 -7.5946777E-04 1,midg,midg; igrid,midg,midg 1.5185522E-02 8.3793830E-03 gauss-seidel spectral radius is 0.9982771 estimated iterations to convergence 191 setup time was (sec) 1.000000 now iterating at: 08:16:38 rms-change max change #iterations 4.378134 155.2860 at 10iterations 1.867573 55.08804 at 20iterations 0.7964016 23.33319 at 30iterations 0.3398616 10.22288 at 40iterations 0.1449144 4.894859 at 50iterations 6.1936151E-02 1.843184 at 60iterations 2.6413357E-02 0.7523575 at 70iterations 1.1322783E-02 0.3247223 at 80iterations 4.8503238E-03 0.1940775 at 90iterations 2.0946553E-03 6.1281204E-02 at 100iterations 9.1095746E-04 2.6807785E-02 at 110iterations 4.0518175E-04 1.3561249E-02 at 120iterations finished qdiffx linear iterations at : 08:16:45 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 4.0518175E-04 1.3561249E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 08:16:45 7.557u 0.163s 0:08.04 95.8% 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 Sun Oct 9 2011 at 08:16:45 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5631 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.344642 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): -22.33700 45.98900 ymin,ymax (A): 4.810000 68.06001 zmin,zma (A): -110.9840 -43.64500 x,y,z range (A): 68.32600 63.25000 67.33900 scale (grids/A): 2.344642 object centre (A): 11.82600 36.43500 -77.31450 number of atom coordinates read : 5631 total number of charged atoms : 5463 net assigned charge : -0.4999426 assigned positive charge : 847.9505 centred at (gu) : 92.81924 93.45406 86.10805 assigned negative charge : -848.4578 centred at (gu) : 92.92912 93.36064 85.43591 start vw surface at 0.2200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 252339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 114022 mr = 180275 m= 30337 mr = 88780 m= 4605 mr = 22395 m= 272 mr = 2935 m= 3 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 9706 time to turn everything in is 1.780000 number of dielectric boundary points 107071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 43602 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) : 1.563095 object centre at (A) : 11.82600 36.43500 -77.31450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5779328 0.2974592 midg,1,midg; midg,igrid,midg 1.1000148E-02 3.9911214E-02 1,midg,midg; igrid,midg,midg 0.1954944 0.3819824 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 2.080000 now iterating at: 08:16:47 rms-change max change #iterations 11.68068 318.1226 at 10iterations 6.881546 144.3804 at 20iterations 4.034852 78.38745 at 30iterations 2.353323 49.83348 at 40iterations 1.366111 25.03004 at 50iterations 0.7918978 13.93923 at 60iterations 0.4580252 7.883663 at 70iterations 0.2640380 4.823486 at 80iterations 0.1520827 2.445457 at 90iterations 8.7438866E-02 1.517168 at 100iterations 5.0279908E-02 0.8636334 at 110iterations 2.8829370E-02 0.5003564 at 120iterations 1.6586529E-02 0.2745609 at 130iterations 9.4875582E-03 0.1593451 at 140iterations 5.4381019E-03 0.1119347 at 150iterations 3.1163523E-03 5.1558971E-02 at 160iterations 1.7875941E-03 3.0807495E-02 at 170iterations 1.0255347E-03 1.7972946E-02 at 180iterations finished qdiffx linear iterations at : 08:16:57 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 1.0255347E-03 1.7972946E-02 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.15000 DelPhi exited at 08:16:58 12.150u 0.167s 0:12.65 97.3% 0+0k 0+0io 0pf+0w