Sat Oct 8 23:30:59 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 8 2011 at 23:31:00 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6020225 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 0.6020225 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.514030 assigned positive charge : 371.9601 centred at (gu) : 91.46128 90.98457 90.49818 assigned negative charge : -362.4469 centred at (gu) : 91.39308 90.88061 90.42968 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6100 nv = 96 ne = 84 npr = 50518 no. pairs analyzed = 50518 no. exposed pairs = 3329 no. arc points = 23735 no. surface atoms = 1113 nbur = 1409 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3119 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2334 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7612 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5812890E-09 7.4932807E-09 midg,1,midg; midg,igrid,midg 3.9110443E-10 9.9389323E-09 1,midg,midg; igrid,midg,midg 1.3128977E-09 9.2966106E-09 gauss-seidel spectral radius is 0.9857178 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 23:31:00 rms-change max change #iterations 0.1033545 16.65776 at 10iterations 8.9797433E-03 1.651055 at 20iterations 7.7450089E-04 0.1219702 at 30iterations 7.5116928E-05 1.0999680E-02 at 40iterations 9.5872228E-06 1.6412735E-03 at 50iterations finished qdiffx linear iterations at : 23:31:03 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 9.5872228E-06 1.6412735E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 23:31:04 3.736u 0.223s 0:04.25 92.9% 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 Sat Oct 8 2011 at 23:31:04 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806067 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 1.806067 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.514030 assigned positive charge : 371.9601 centred at (gu) : 94.38337 92.95323 91.49419 assigned negative charge : -362.4469 centred at (gu) : 94.17912 92.64165 91.28913 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23735 grid for indexing accessible points = 1.400000 m= 21900 mr = 43748 m= 3087 mr = 15416 m= 168 mr = 1789 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 0.3400000 number of dielectric boundary points 29949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18611 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) : 0.6020225 object centre at (A) : -2.897000 29.07400 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1713709E-02 2.5246909E-02 midg,1,midg; midg,igrid,midg -7.1700884E-04 2.0395935E-02 1,midg,midg; igrid,midg,midg -8.1465952E-03 4.7309883E-02 gauss-seidel spectral radius is 0.9984822 estimated iterations to convergence 204 setup time was (sec) 0.5800000 now iterating at: 23:31:05 rms-change max change #iterations 3.689456 182.4352 at 10iterations 1.643825 65.40370 at 20iterations 0.7384046 25.43512 at 30iterations 0.3319908 10.69063 at 40iterations 0.1484404 5.309219 at 50iterations 6.6623457E-02 2.324466 at 60iterations 2.9995345E-02 0.9707451 at 70iterations 1.3428231E-02 0.5117826 at 80iterations 6.0228254E-03 0.2084198 at 90iterations 2.7129841E-03 8.9872360E-02 at 100iterations 1.2199591E-03 4.4623375E-02 at 110iterations 5.4879638E-04 1.8313408E-02 at 120iterations finished qdiffx linear iterations at : 23:31:12 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 5.4879638E-04 1.8313408E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 23:31:13 8.448u 0.234s 0:09.01 96.2% 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 8 2011 at 23:31:13 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2522 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.709101 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): -32.46400 26.67000 ymin,ymax (A): 8.249000 49.89900 zmin,zma (A): -11.45700 43.35800 x,y,z range (A): 59.13400 41.65000 54.81500 scale (grids/A): 2.709101 object centre (A): -2.897000 29.07400 15.95050 number of atom coordinates read : 2522 total number of charged atoms : 2385 net assigned charge : 9.514030 assigned positive charge : 371.9601 centred at (gu) : 96.57499 94.42967 92.24128 assigned negative charge : -362.4469 centred at (gu) : 96.26871 93.96252 91.93364 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23735 grid for indexing accessible points = 1.400000 m= 72129 mr = 107027 m= 24111 mr = 56983 m= 5344 mr = 18807 m= 687 mr = 3917 m= 35 mr = 436 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2958 time to turn everything in is 0.8300000 number of dielectric boundary points 67570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 19077 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) : 1.806067 object centre at (A) : -2.897000 29.07400 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5146781 0.2795886 midg,1,midg; midg,igrid,midg -1.7169798E-03 0.2168887 1,midg,midg; igrid,midg,midg -0.1230073 0.5200973 gauss-seidel spectral radius is 0.9992236 estimated iterations to convergence 283 setup time was (sec) 1.080000 now iterating at: 23:31:14 rms-change max change #iterations 8.997738 262.6384 at 10iterations 5.221907 134.8221 at 20iterations 3.009382 96.42953 at 30iterations 1.726887 42.72070 at 40iterations 0.9917842 24.44787 at 50iterations 0.5651590 12.50071 at 60iterations 0.3229695 6.771563 at 70iterations 0.1840674 4.052425 at 80iterations 0.1046849 2.115847 at 90iterations 5.9460554E-02 1.234274 at 100iterations 3.3824805E-02 0.6725152 at 110iterations 1.9223344E-02 0.3958073 at 120iterations 1.0888256E-02 0.2223650 at 130iterations 6.1841509E-03 0.1371250 at 140iterations 3.5175632E-03 6.9572449E-02 at 150iterations 1.9906985E-03 3.7173271E-02 at 160iterations 1.1298970E-03 1.9886017E-02 at 170iterations 6.3993107E-04 1.3484955E-02 at 180iterations finished qdiffx linear iterations at : 23:31:26 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 6.3993107E-04 1.3484955E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 23:31:27 12.995u 0.231s 0:13.93 94.9% 0+0k 0+0io 0pf+0w