Sat Oct 15 12:25:05 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 Sat Oct 15 2011 at 12:25:05 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 !!! WARNING: SEP 499 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5033225 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 0.5033225 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5150 net assigned charge : 14.02497 assigned positive charge : 802.9952 centred at (gu) : 88.57605 90.86532 90.45831 assigned negative charge : -788.9772 centred at (gu) : 88.53114 90.91053 90.42738 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8537 nv = 96 ne = 84 npr = 107569 no. pairs analyzed = 107569 no. exposed pairs = 6759 no. arc points = 46480 no. surface atoms = 2260 nbur = 3093 mkacc time = 0.2900000 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 = 1.708000 m= 314 mr = 4440 m= 0 mr = 11 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4437 ## 635 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 11472 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1432880E-11 2.3579047E-10 midg,1,midg; midg,igrid,midg 1.8988487E-10 6.1513343E-11 1,midg,midg; igrid,midg,midg 7.1279170E-11 1.6373292E-10 gauss-seidel spectral radius is 0.9798566 estimated iterations to convergence 58 setup time was (sec) 0.9000000 now iterating at: 12:25:06 rms-change max change #iterations 6.5165058E-02 11.28647 at 10iterations 5.7059806E-03 0.7707977 at 20iterations 1.6694439E-03 0.2286835 at 30iterations 6.2450476E-04 7.9196930E-02 at 40iterations 2.3820513E-04 2.8560638E-02 at 50iterations finished qdiffx linear iterations at : 12:25:11 total time elapsed so far: 5.460000 # loops : 50 mean,max change (kT/e) : 2.3820513E-04 2.8560638E-02 energy calculations done at 5.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.630000 DelPhi exited at 12:25:11 5.631u 0.453s 0:06.38 95.2% 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 12:25:11 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 !!! WARNING: SEP 499 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.509968 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 1.509968 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5150 net assigned charge : 14.02497 assigned positive charge : 802.9952 centred at (gu) : 85.72610 92.59384 91.37325 assigned negative charge : -788.9772 centred at (gu) : 85.59290 92.73087 91.28164 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 97743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27560 mr = 67463 m= 2218 mr = 17982 m= 44 mr = 899 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 41221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 566 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 38469 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) : 0.5033225 object centre at (A) : 38.04000 19.09000 26.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2209593E-02 4.4735852E-03 midg,1,midg; midg,igrid,midg 8.8463882E-03 7.1266457E-03 1,midg,midg; igrid,midg,midg 3.8205259E-02 2.9488441E-02 gauss-seidel spectral radius is 0.9981099 estimated iterations to convergence 183 setup time was (sec) 1.190000 now iterating at: 12:25:13 rms-change max change #iterations 3.905343 183.9273 at 10iterations 1.592980 54.80133 at 20iterations 0.6526812 20.69043 at 30iterations 0.2664824 8.329927 at 40iterations 0.1100027 3.302307 at 50iterations 4.5348193E-02 1.347565 at 60iterations 1.9008717E-02 0.5698357 at 70iterations 8.2634268E-03 0.2843342 at 80iterations 3.8165459E-03 0.1109848 at 90iterations 2.0013808E-03 6.3598633E-02 at 100iterations 1.1875130E-03 3.1799316E-02 at 110iterations 7.7249232E-04 1.9607544E-02 at 120iterations finished qdiffx linear iterations at : 12:25:25 total time elapsed so far: 13.19000 # loops : 120 mean,max change (kT/e) : 7.7249232E-04 1.9607544E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 12:25:25 13.363u 0.528s 0:14.24 97.4% 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 12:25:25 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5353 !!! WARNING: SEP 499 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.264951 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): 2.675000 73.40500 ymin,ymax (A): -10.32900 48.50900 zmin,zma (A): -7.890000 60.45700 x,y,z range (A): 70.73000 58.83800 68.34700 scale (grids/A): 2.264951 object centre (A): 38.04000 19.09000 26.28350 number of atom coordinates read : 5353 total number of charged atoms : 5150 net assigned charge : 14.02497 assigned positive charge : 802.9952 centred at (gu) : 83.58853 93.89037 92.05946 assigned negative charge : -788.9772 centred at (gu) : 83.38916 94.09634 91.92251 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 228111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46480 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 99897 mr = 166125 m= 24168 mr = 77287 m= 3087 mr = 17159 m= 131 mr = 1794 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 93004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 41044 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) : 1.509968 object centre at (A) : 38.04000 19.09000 26.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2589617 0.1334091 midg,1,midg; midg,igrid,midg 0.1605896 0.1418526 1,midg,midg; igrid,midg,midg 0.6625530 0.7383474 gauss-seidel spectral radius is 0.9991750 estimated iterations to convergence 275 setup time was (sec) 2.470000 now iterating at: 12:25:28 rms-change max change #iterations 10.71515 255.7168 at 10iterations 6.181650 171.5969 at 20iterations 3.556688 82.12750 at 30iterations 2.021712 51.29417 at 40iterations 1.148163 24.43914 at 50iterations 0.6472103 14.43152 at 60iterations 0.3647220 6.980164 at 70iterations 0.2053984 3.640984 at 80iterations 0.1154429 2.367469 at 90iterations 6.4630687E-02 1.265326 at 100iterations 3.6364496E-02 0.6822433 at 110iterations 2.0391252E-02 0.3900452 at 120iterations 1.1465954E-02 0.1997166 at 130iterations 6.4768321E-03 0.1171913 at 140iterations 3.6955180E-03 6.8665504E-02 at 150iterations 2.1469078E-03 4.0453911E-02 at 160iterations 1.2844396E-03 2.2624969E-02 at 170iterations 8.0256630E-04 1.4788628E-02 at 180iterations finished qdiffx linear iterations at : 12:25:49 total time elapsed so far: 22.61000 # loops : 180 mean,max change (kT/e) : 8.0256630E-04 1.4788628E-02 energy calculations done at 22.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.78000 DelPhi exited at 12:25:49 22.785u 0.546s 0:23.66 98.5% 0+0k 0+0io 0pf+0w