Mon Oct 10 17:02:03 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 Mon Oct 10 2011 at 17:02:03 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLM 103 has a net charge of -0.0940 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: 0.5785607 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 0.5785607 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2693 net assigned charge : 0.9060315 assigned positive charge : 422.0924 centred at (gu) : 89.74570 89.19923 89.86060 assigned negative charge : -421.1873 centred at (gu) : 89.70650 89.34297 89.96587 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6329 nv = 96 ne = 84 npr = 57198 no. pairs analyzed = 57198 no. exposed pairs = 3528 no. arc points = 25662 no. surface atoms = 1191 nbur = 1647 mkacc time = 9.9999994E-02 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 = 1.484000 m= 290 mr = 3324 m= 1 mr = 9 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 0.2000000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2649 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3081861E-09 -1.8911608E-09 midg,1,midg; midg,igrid,midg 3.6039460E-09 -2.2661291E-09 1,midg,midg; igrid,midg,midg -6.5782685E-10 8.8621721E-10 gauss-seidel spectral radius is 0.9845743 estimated iterations to convergence 66 setup time was (sec) 0.4000000 now iterating at: 17:02:04 rms-change max change #iterations 9.5612377E-02 19.41401 at 10iterations 7.4680350E-03 1.219973 at 20iterations 5.7065167E-04 8.6982727E-02 at 30iterations 4.4004511E-05 6.2446594E-03 at 40iterations 3.4321035E-06 5.9223175E-04 at 50iterations finished qdiffx linear iterations at : 17:02:07 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 3.4321035E-06 5.9223175E-04 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 17:02:08 3.735u 0.202s 0:04.73 83.0% 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 17:02:08 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.735682 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 1.735682 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2693 net assigned charge : 0.9060315 assigned positive charge : 422.0924 centred at (gu) : 89.23599 87.59693 89.58095 assigned negative charge : -421.1873 centred at (gu) : 89.11912 88.02837 89.89725 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69742 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 22493 mr = 47429 m= 2676 mr = 15793 m= 89 mr = 1464 m= 0 mr = 14 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1461 time to turn everything in is 0.3500000 number of dielectric boundary points 30300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 259 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 20959 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) : 0.5785607 object centre at (A) : 14.32850 2.857000 44.58800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6040487E-02 -5.0705075E-03 midg,1,midg; midg,igrid,midg 8.9497138E-03 -1.8286755E-02 1,midg,midg; igrid,midg,midg -2.4655489E-03 -3.5544690E-03 gauss-seidel spectral radius is 0.9983909 estimated iterations to convergence 198 setup time was (sec) 0.6200000 now iterating at: 17:02:09 rms-change max change #iterations 3.738045 169.5705 at 10iterations 1.632926 59.34059 at 20iterations 0.7135374 24.61822 at 30iterations 0.3150589 9.898910 at 40iterations 0.1371474 5.042955 at 50iterations 6.0531832E-02 2.146760 at 60iterations 2.6436560E-02 0.8371425 at 70iterations 1.1628758E-02 0.4528728 at 80iterations 5.1026889E-03 0.1823131 at 90iterations 2.2410471E-03 7.1838379E-02 at 100iterations 9.8187523E-04 3.1167984E-02 at 110iterations 4.3329518E-04 1.5097082E-02 at 120iterations finished qdiffx linear iterations at : 17:02:17 total time elapsed so far: 8.830000 # loops : 120 mean,max change (kT/e) : 4.3329518E-04 1.5097082E-02 energy calculations done at 8.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.960000 DelPhi exited at 17:02:18 8.966u 0.279s 0:09.72 94.9% 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 Mon Oct 10 2011 at 17:02:18 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2838 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.603523 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): -10.93900 39.59600 ymin,ymax (A): -24.06100 29.77500 zmin,zma (A): 13.82200 75.35400 x,y,z range (A): 50.53500 53.83600 61.53201 scale (grids/A): 2.603523 object centre (A): 14.32850 2.857000 44.58800 number of atom coordinates read : 2838 total number of charged atoms : 2693 net assigned charge : 0.9060315 assigned positive charge : 422.0924 centred at (gu) : 88.85386 86.39519 89.37115 assigned negative charge : -421.1873 centred at (gu) : 88.67855 87.04251 89.84590 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25662 grid for indexing accessible points = 1.400000 m= 76232 mr = 115634 m= 23559 mr = 60983 m= 4566 mr = 18131 m= 381 mr = 3164 m= 7 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 4965 time to turn everything in is 0.8400000 number of dielectric boundary points 68315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 21538 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) : 1.735682 object centre at (A) : 14.32850 2.857000 44.58800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3053095 -6.5344848E-02 midg,1,midg; midg,igrid,midg 9.7284377E-02 -0.2205438 1,midg,midg; igrid,midg,midg -6.2896766E-02 -5.4847196E-02 gauss-seidel spectral radius is 0.9992000 estimated iterations to convergence 279 setup time was (sec) 1.070000 now iterating at: 17:02:19 rms-change max change #iterations 9.127016 291.7704 at 10iterations 5.196759 135.8410 at 20iterations 2.942434 92.64383 at 30iterations 1.657257 44.47486 at 40iterations 0.9350696 19.88363 at 50iterations 0.5264603 11.49592 at 60iterations 0.2956299 6.137453 at 70iterations 0.1661345 3.580229 at 80iterations 9.3500420E-02 1.830053 at 90iterations 5.2350316E-02 1.062962 at 100iterations 2.9406587E-02 0.5649109 at 110iterations 1.6533038E-02 0.3325496 at 120iterations 9.2595834E-03 0.1903725 at 130iterations 5.2088671E-03 0.1091614 at 140iterations 2.9190893E-03 5.8959961E-02 at 150iterations 1.6394840E-03 3.2211304E-02 at 160iterations 9.1910531E-04 1.8360138E-02 at 170iterations 5.1606330E-04 9.4652176E-03 at 180iterations finished qdiffx linear iterations at : 17:02:31 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 5.1606330E-04 9.4652176E-03 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 17:02:33 13.362u 0.285s 0:15.00 90.9% 0+0k 0+0io 0pf+0w