Mon Oct 10 14:38:28 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 Mon Oct 10 2011 at 14:38:28 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6051334 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 0.6051334 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 364.9321 centred at (gu) : 90.14236 89.41827 89.24854 assigned negative charge : -368.9324 centred at (gu) : 89.91186 89.47008 89.28098 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 49876 no. pairs analyzed = 49876 no. exposed pairs = 3365 no. arc points = 23600 no. surface atoms = 1136 nbur = 1357 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 311 mr = 3133 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5422663E-10 -2.8540685E-09 midg,1,midg; midg,igrid,midg 6.4417811E-11 -3.6579690E-09 1,midg,midg; igrid,midg,midg -1.1289014E-08 7.3061108E-09 gauss-seidel spectral radius is 0.9858629 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 14:38:29 rms-change max change #iterations 0.1078483 18.78041 at 10iterations 9.4697215E-03 1.740189 at 20iterations 7.9554779E-04 0.1195221 at 30iterations 6.9815702E-05 1.2113094E-02 at 40iterations 6.0507355E-06 9.9563599E-04 at 50iterations finished qdiffx linear iterations at : 14:38:33 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 6.0507355E-06 9.9563599E-04 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 14:38:33 4.501u 0.428s 0:05.34 92.1% 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 14:38:34 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.815400 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 1.815400 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 364.9321 centred at (gu) : 90.42655 88.25415 87.74511 assigned negative charge : -368.9324 centred at (gu) : 89.73545 88.40980 87.84254 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 67275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 22279 mr = 44976 m= 2841 mr = 15465 m= 123 mr = 1370 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 30681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 18231 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) : 0.6051334 object centre at (A) : 18.17750 31.33500 12.45450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0764077E-03 -1.1540259E-02 midg,1,midg; midg,igrid,midg -1.2111515E-02 1.6860814E-04 1,midg,midg; igrid,midg,midg -3.6209218E-02 8.3528291E-03 gauss-seidel spectral radius is 0.9984953 estimated iterations to convergence 204 setup time was (sec) 1.010000 now iterating at: 14:38:35 rms-change max change #iterations 3.735316 186.1150 at 10iterations 1.666313 58.19189 at 20iterations 0.7552785 27.14227 at 30iterations 0.3386180 11.75788 at 40iterations 0.1525215 5.126968 at 50iterations 6.9111273E-02 2.446497 at 60iterations 3.0921264E-02 1.138329 at 70iterations 1.3963364E-02 0.4886510 at 80iterations 6.2993681E-03 0.2032166 at 90iterations 2.8441146E-03 9.9695921E-02 at 100iterations 1.2749417E-03 4.5042038E-02 at 110iterations 5.7646696E-04 2.0635605E-02 at 120iterations finished qdiffx linear iterations at : 14:38:44 total time elapsed so far: 10.18000 # loops : 120 mean,max change (kT/e) : 5.7646696E-04 2.0635605E-02 energy calculations done at 10.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 14:38:45 10.411u 0.490s 0:11.17 97.5% 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 14:38:45 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2493 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.723100 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): -7.758000 44.11300 ymin,ymax (A): 1.920000 60.75000 zmin,zma (A): -14.35100 39.26000 x,y,z range (A): 51.87100 58.83000 53.61100 scale (grids/A): 2.723100 object centre (A): 18.17750 31.33500 12.45450 number of atom coordinates read : 2493 total number of charged atoms : 2334 net assigned charge : -3.999990 assigned positive charge : 364.9321 centred at (gu) : 90.63974 87.38103 86.61745 assigned negative charge : -368.9324 centred at (gu) : 89.60300 87.61457 86.76363 start vw surface at 0.1500000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 155746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23600 grid for indexing accessible points = 1.400000 m= 74781 mr = 109911 m= 23818 mr = 59204 m= 4595 mr = 17823 m= 472 mr = 2997 m= 46 mr = 245 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 69257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 18671 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) : 1.815400 object centre at (A) : 18.17750 31.33500 12.45450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2319005E-02 -0.1797203 midg,1,midg; midg,igrid,midg -0.1683388 5.1935136E-02 1,midg,midg; igrid,midg,midg -0.4071252 6.6017084E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 2.170000 now iterating at: 14:38:47 rms-change max change #iterations 9.091412 270.7284 at 10iterations 5.312228 126.2935 at 20iterations 3.065441 95.95934 at 30iterations 1.762636 38.34486 at 40iterations 1.012715 24.94036 at 50iterations 0.5778636 12.17560 at 60iterations 0.3300763 7.117970 at 70iterations 0.1882768 4.113111 at 80iterations 0.1070975 2.285507 at 90iterations 6.0963400E-02 1.319511 at 100iterations 3.4679566E-02 0.7347336 at 110iterations 1.9670466E-02 0.3807411 at 120iterations 1.1153479E-02 0.2047138 at 130iterations 6.3368082E-03 0.1277628 at 140iterations 3.5933191E-03 8.1132412E-02 at 150iterations 2.0332288E-03 4.3640137E-02 at 160iterations 1.1545790E-03 2.7552605E-02 at 170iterations 6.5338600E-04 1.3280869E-02 at 180iterations finished qdiffx linear iterations at : 14:39:07 total time elapsed so far: 21.47000 # loops : 180 mean,max change (kT/e) : 6.5338600E-04 1.3280869E-02 energy calculations done at 21.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.69000 DelPhi exited at 14:39:07 21.695u 0.524s 0:22.54 98.5% 0+0k 0+0io 0pf+0w