Sat Oct 8 16:05:38 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 Sat Oct 8 2011 at 16:05:38 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 = 2298 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: 0.6470492 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 0.6470492 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 90.52154 88.86184 90.28797 assigned negative charge : -338.3788 centred at (gu) : 90.57138 88.98370 90.32850 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6602 nv = 96 ne = 84 npr = 45638 no. pairs analyzed = 45638 no. exposed pairs = 2919 no. arc points = 20572 no. surface atoms = 996 nbur = 1302 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3595 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2000 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1238090E-08 2.0778925E-09 midg,1,midg; midg,igrid,midg 2.7743484E-08 -6.3392367E-09 1,midg,midg; igrid,midg,midg 1.1717711E-08 8.6978508E-10 gauss-seidel spectral radius is 0.9876009 estimated iterations to convergence 73 setup time was (sec) 0.4900000 now iterating at: 16:05:38 rms-change max change #iterations 0.1432794 21.88526 at 10iterations 1.4586490E-02 2.580006 at 20iterations 1.5136834E-03 0.1856632 at 30iterations 1.7698022E-04 2.5305986E-02 at 40iterations 3.0216524E-05 4.8365593E-03 at 50iterations finished qdiffx linear iterations at : 16:05:41 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 3.0216524E-05 4.8365593E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 16:05:41 3.069u 0.158s 0:03.51 91.4% 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 8 2011 at 16:05:41 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 = 2298 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: 1.941148 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 1.941148 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 91.56409 86.58516 90.86375 assigned negative charge : -338.3788 centred at (gu) : 91.71407 86.95106 90.98535 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70529 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20572 grid for indexing accessible points = 1.400000 m= 26132 mr = 48439 m= 4714 mr = 19253 m= 309 mr = 3075 m= 3 mr = 133 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 437 time to turn everything in is 0.5200000 number of dielectric boundary points 30787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17565 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) : 0.6470492 object centre at (A) : 22.35750 6.377500 9.126499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0643285E-02 -4.8989961E-03 midg,1,midg; midg,igrid,midg 2.6688501E-02 -3.1619333E-03 1,midg,midg; igrid,midg,midg 1.0278155E-02 -4.3559864E-02 gauss-seidel spectral radius is 0.9986603 estimated iterations to convergence 216 setup time was (sec) 0.8100000 now iterating at: 16:05:42 rms-change max change #iterations 4.115177 184.6354 at 10iterations 1.934824 70.90248 at 20iterations 0.9143232 34.50410 at 30iterations 0.4317776 13.42734 at 40iterations 0.2034301 6.573524 at 50iterations 9.6422695E-02 3.020203 at 60iterations 4.5504980E-02 1.327871 at 70iterations 2.1514051E-02 0.6589959 at 80iterations 1.0147930E-02 0.3247528 at 90iterations 4.7877715E-03 0.1428833 at 100iterations 2.2721256E-03 7.1177244E-02 at 110iterations 1.0793706E-03 3.7085533E-02 at 120iterations finished qdiffx linear iterations at : 16:05:49 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.0793706E-03 3.7085533E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 16:05:50 7.818u 0.236s 0:08.39 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 Sat Oct 8 2011 at 16:05:50 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 = 2298 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: 2.911721 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): -1.762000 46.47700 ymin,ymax (A): -16.42400 29.17900 zmin,zma (A): -18.38300 36.63600 x,y,z range (A): 48.23900 45.60300 55.01900 scale (grids/A): 2.911721 object centre (A): 22.35750 6.377500 9.126499 number of atom coordinates read : 2298 total number of charged atoms : 2230 net assigned charge : 4.000001 assigned positive charge : 342.3781 centred at (gu) : 92.34594 84.87756 91.29546 assigned negative charge : -338.3788 centred at (gu) : 92.57117 85.42651 91.47785 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163090 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20572 grid for indexing accessible points = 1.400000 m= 83419 mr = 117751 m= 31845 mr = 67968 m= 8635 mr = 25699 m= 1360 mr = 6640 m= 107 mr = 914 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 1477 time to turn everything in is 1.310000 number of dielectric boundary points 69422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 17839 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) : 1.941148 object centre at (A) : 22.35750 6.377500 9.126499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1792690 -9.5147960E-02 midg,1,midg; midg,igrid,midg 0.1974163 -5.5328060E-02 1,midg,midg; igrid,midg,midg 0.1145270 -0.5867480 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 1.630000 now iterating at: 16:05:52 rms-change max change #iterations 9.580351 407.6935 at 10iterations 5.631348 130.9375 at 20iterations 3.280639 64.57562 at 30iterations 1.916234 38.53219 at 40iterations 1.111837 20.30429 at 50iterations 0.6453676 15.61353 at 60iterations 0.3745832 7.279819 at 70iterations 0.2161231 4.776017 at 80iterations 0.1252055 2.652786 at 90iterations 7.2404295E-02 1.345955 at 100iterations 4.1773655E-02 0.8517761 at 110iterations 2.4107860E-02 0.4668905 at 120iterations 1.3932204E-02 0.2493620 at 130iterations 8.0150124E-03 0.1450729 at 140iterations 4.6333023E-03 7.9799652E-02 at 150iterations 2.6642114E-03 5.0133705E-02 at 160iterations 1.5380437E-03 2.8293610E-02 at 170iterations 8.8807603E-04 1.7332077E-02 at 180iterations finished qdiffx linear iterations at : 16:06:03 total time elapsed so far: 12.57000 # loops : 180 mean,max change (kT/e) : 8.8807603E-04 1.7332077E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 16:06:03 12.738u 0.288s 0:13.31 97.7% 0+0k 0+0io 0pf+0w