Mon Oct 10 09:51:04 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 09:51:04 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIT 232 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5812909 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 0.5812909 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.014012 assigned positive charge : 419.1239 centred at (gu) : 89.09218 89.42749 87.68038 assigned negative charge : -415.1104 centred at (gu) : 89.22590 89.32493 87.48054 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6458 nv = 96 ne = 84 npr = 54831 no. pairs analyzed = 54831 no. exposed pairs = 4295 no. arc points = 31680 no. surface atoms = 1404 nbur = 1429 mkacc time = 0.1300000 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 = 1.512000 m= 328 mr = 2811 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3087 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8127 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8933538E-09 3.0131004E-09 midg,1,midg; midg,igrid,midg -1.3756021E-09 2.7722793E-09 1,midg,midg; igrid,midg,midg 4.7253859E-09 -1.5044158E-09 gauss-seidel spectral radius is 0.9847301 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 09:51:05 rms-change max change #iterations 9.4695620E-02 16.32296 at 10iterations 7.1388381E-03 1.458565 at 20iterations 5.7663565E-04 0.1020432 at 30iterations 4.7803729E-05 6.8550110E-03 at 40iterations 5.0009626E-06 6.2179565E-04 at 50iterations finished qdiffx linear iterations at : 09:51:08 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 5.0009626E-06 6.2179565E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 09:51:09 3.639u 0.214s 0:04.13 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 Mon Oct 10 2011 at 09:51:09 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIT 232 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.743873 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 1.743873 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.014012 assigned positive charge : 419.1239 centred at (gu) : 87.27618 88.28191 83.04070 assigned negative charge : -415.1104 centred at (gu) : 87.67748 87.97440 82.44119 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31680 grid for indexing accessible points = 1.400000 m= 21309 mr = 42374 m= 2771 mr = 13287 m= 120 mr = 1221 m= 0 mr = 23 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.5500000 number of dielectric boundary points 36781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 20823 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) : 0.5812909 object centre at (A) : 9.392999 -33.96100 26.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1412592E-02 1.8949615E-02 midg,1,midg; midg,igrid,midg 1.9378917E-02 3.8419813E-02 1,midg,midg; igrid,midg,midg 1.6066043E-02 -3.0714055E-03 gauss-seidel spectral radius is 0.9984211 estimated iterations to convergence 200 setup time was (sec) 0.8700000 now iterating at: 09:51:10 rms-change max change #iterations 3.728687 158.2683 at 10iterations 1.640075 78.96529 at 20iterations 0.7199556 25.93755 at 30iterations 0.3186080 10.52366 at 40iterations 0.1397678 4.715424 at 50iterations 6.1901942E-02 2.098297 at 60iterations 2.7176270E-02 0.9339256 at 70iterations 1.2016099E-02 0.4168282 at 80iterations 5.2985470E-03 0.1881814 at 90iterations 2.3398381E-03 8.3064079E-02 at 100iterations 1.0331994E-03 3.3584595E-02 at 110iterations 4.5457526E-04 1.6254425E-02 at 120iterations finished qdiffx linear iterations at : 09:51:17 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 4.5457526E-04 1.6254425E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 09:51:18 8.351u 0.252s 0:08.90 96.6% 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 09:51:18 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIT 232 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.615809 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): -17.41200 36.19800 ymin,ymax (A): -63.20800 -4.714000 zmin,zma (A): -4.153000 57.09000 x,y,z range (A): 53.61000 58.49400 61.24300 scale (grids/A): 2.615809 object centre (A): 9.392999 -33.96100 26.46850 number of atom coordinates read : 2833 total number of charged atoms : 2681 net assigned charge : 4.014012 assigned positive charge : 419.1239 centred at (gu) : 85.91414 87.42273 79.56100 assigned negative charge : -415.1104 centred at (gu) : 86.51614 86.96157 78.66173 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 160280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31680 grid for indexing accessible points = 1.400000 m= 70951 mr = 104605 m= 22282 mr = 52434 m= 4371 mr = 15583 m= 472 mr = 2612 m= 17 mr = 233 m= 0 mr = 4 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 1.320000 number of dielectric boundary points 82902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 21438 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) : 1.743873 object centre at (A) : 9.392999 -33.96100 26.46850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2295225 0.2818325 midg,1,midg; midg,igrid,midg 0.5666707 0.5107856 1,midg,midg; igrid,midg,midg 0.1575889 -9.5925387E-03 gauss-seidel spectral radius is 0.9992261 estimated iterations to convergence 284 setup time was (sec) 1.670000 now iterating at: 09:51:19 rms-change max change #iterations 9.450260 272.0454 at 10iterations 5.579767 153.3918 at 20iterations 3.263052 94.10172 at 30iterations 1.889877 53.60923 at 40iterations 1.085142 30.68717 at 50iterations 0.6229451 14.21055 at 60iterations 0.3568150 9.531998 at 70iterations 0.2043776 5.216053 at 80iterations 0.1164645 2.800219 at 90iterations 6.6411987E-02 1.551490 at 100iterations 3.7871759E-02 0.8626401 at 110iterations 2.1514799E-02 0.5017732 at 120iterations 1.2227254E-02 0.2809560 at 130iterations 6.9411779E-03 0.1570740 at 140iterations 3.9405986E-03 7.7384949E-02 at 150iterations 2.2440839E-03 4.3925762E-02 at 160iterations 1.2696575E-03 2.6914597E-02 at 170iterations 7.2128605E-04 1.5179634E-02 at 180iterations finished qdiffx linear iterations at : 09:51:33 total time elapsed so far: 14.93000 # loops : 180 mean,max change (kT/e) : 7.2128605E-04 1.5179634E-02 energy calculations done at 14.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 09:51:33 15.119u 0.256s 0:15.65 98.1% 0+0k 0+0io 0pf+0w