Tue Oct 11 07:09:14 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 Tue Oct 11 2011 at 07:09:14 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3808 !!! WARNING: HIR 170 has a net charge of 0.5140 !!! WARNING: GLM 188 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: HIR 230 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5528379 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 0.5528379 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3659 net assigned charge : 6.959031 assigned positive charge : 579.3752 centred at (gu) : 90.37682 90.60815 90.55305 assigned negative charge : -572.4187 centred at (gu) : 90.24685 90.61475 90.55056 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7416 nv = 96 ne = 84 npr = 79561 no. pairs analyzed = 79561 no. exposed pairs = 4310 no. arc points = 30269 no. surface atoms = 1454 nbur = 2354 mkacc time = 0.2300000 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 = 1.568000 m= 288 mr = 4179 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3090 ## 397 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9745 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6725951E-10 6.7014144E-10 midg,1,midg; midg,igrid,midg 5.4735355E-10 5.6241090E-10 1,midg,midg; igrid,midg,midg -8.1383622E-10 2.1610345E-09 gauss-seidel spectral radius is 0.9831807 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 07:09:15 rms-change max change #iterations 8.8063784E-02 11.87109 at 10iterations 6.6230022E-03 0.9384766 at 20iterations 8.0109283E-04 0.1347713 at 30iterations 2.0126367E-04 3.7063599E-02 at 40iterations 5.6780391E-05 1.0557175E-02 at 50iterations finished qdiffx linear iterations at : 07:09:18 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 5.6780391E-05 1.0557175E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 07:09:19 4.270u 0.257s 0:04.85 93.1% 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 Tue Oct 11 2011 at 07:09:19 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3808 !!! WARNING: HIR 170 has a net charge of 0.5140 !!! WARNING: GLM 188 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: HIR 230 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.658514 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 1.658514 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3659 net assigned charge : 6.959031 assigned positive charge : 579.3752 centred at (gu) : 91.12885 91.82340 91.65805 assigned negative charge : -572.4187 centred at (gu) : 90.73999 91.84388 91.65128 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26441 mr = 59033 m= 2576 mr = 18982 m= 62 mr = 1364 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 0.7200000 number of dielectric boundary points 32573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 349 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 28051 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) : 0.5528379 object centre at (A) : 24.14500 -27.43750 -5.186502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3984797E-02 5.3952578E-02 midg,1,midg; midg,igrid,midg -8.8908095E-03 -6.9962959E-03 1,midg,midg; igrid,midg,midg -1.6368736E-02 1.7581385E-02 gauss-seidel spectral radius is 0.9983202 estimated iterations to convergence 194 setup time was (sec) 1.030000 now iterating at: 07:09:20 rms-change max change #iterations 3.943755 183.1729 at 10iterations 1.704627 51.38979 at 20iterations 0.7372926 23.81537 at 30iterations 0.3182702 12.52224 at 40iterations 0.1377621 4.078846 at 50iterations 5.9595045E-02 1.912044 at 60iterations 2.5785081E-02 0.7768850 at 70iterations 1.1134058E-02 0.3671665 at 80iterations 4.8491289E-03 0.1613264 at 90iterations 2.1221053E-03 7.1681499E-02 at 100iterations 9.4491011E-04 3.0318260E-02 at 110iterations 4.2919142E-04 1.6626358E-02 at 120iterations finished qdiffx linear iterations at : 07:09:29 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 4.2919142E-04 1.6626358E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 07:09:29 9.566u 0.335s 0:10.44 94.7% 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 Tue Oct 11 2011 at 07:09:29 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3808 !!! WARNING: HIR 170 has a net charge of 0.5140 !!! WARNING: GLM 188 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: HIR 230 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.487771 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): -5.761000 54.05100 ymin,ymax (A): -53.03500 -1.840000 zmin,zma (A): -37.38400 27.01100 x,y,z range (A): 59.81200 51.19500 64.39500 scale (grids/A): 2.487771 object centre (A): 24.14500 -27.43750 -5.186502 number of atom coordinates read : 3808 total number of charged atoms : 3659 net assigned charge : 6.959031 assigned positive charge : 579.3752 centred at (gu) : 91.69290 92.73466 92.48673 assigned negative charge : -572.4187 centred at (gu) : 91.11007 92.76574 92.47678 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 192705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30269 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 91961 mr = 143695 m= 26356 mr = 74872 m= 4019 mr = 20430 m= 249 mr = 2751 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 3788 time to turn everything in is 1.780000 number of dielectric boundary points 73449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 29252 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) : 1.658514 object centre at (A) : 24.14500 -27.43750 -5.186502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3685934 1.354484 midg,1,midg; midg,igrid,midg -0.1448967 -0.1304535 1,midg,midg; igrid,midg,midg -0.2570125 0.2685118 gauss-seidel spectral radius is 0.9991937 estimated iterations to convergence 278 setup time was (sec) 2.110000 now iterating at: 07:09:32 rms-change max change #iterations 10.00048 268.2071 at 10iterations 5.673937 156.6451 at 20iterations 3.211685 70.44901 at 30iterations 1.818623 35.70339 at 40iterations 1.025900 20.40895 at 50iterations 0.5771004 11.61460 at 60iterations 0.3247379 6.091103 at 70iterations 0.1824795 3.160427 at 80iterations 0.1024531 1.870079 at 90iterations 5.7454620E-02 1.055141 at 100iterations 3.2272685E-02 0.6017361 at 110iterations 1.8118612E-02 0.3402195 at 120iterations 1.0174006E-02 0.2020302 at 130iterations 5.7035098E-03 0.1024551 at 140iterations 3.2105802E-03 6.5315247E-02 at 150iterations 1.8030986E-03 3.3538818E-02 at 160iterations 1.0141644E-03 1.7886162E-02 at 170iterations 5.7480938E-04 1.0028839E-02 at 180iterations finished qdiffx linear iterations at : 07:09:46 total time elapsed so far: 16.06000 # loops : 180 mean,max change (kT/e) : 5.7480938E-04 1.0028839E-02 energy calculations done at 16.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.24000 DelPhi exited at 07:09:46 16.240u 0.325s 0:17.17 96.4% 0+0k 0+0io 0pf+0w