Tue Oct 11 07:59:36 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 07:59:36 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4030 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 0.5309708 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 0.5309708 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3877 net assigned charge : 12.15902 assigned positive charge : 620.4102 centred at (gu) : 89.26712 90.35579 89.33270 assigned negative charge : -608.2543 centred at (gu) : 89.27897 90.39063 89.29767 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7337 nv = 96 ne = 84 npr = 78582 no. pairs analyzed = 78582 no. exposed pairs = 5336 no. arc points = 37299 no. surface atoms = 1782 nbur = 2248 mkacc time = 0.1400000 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 = 1.624000 m= 276 mr = 3678 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3817 ## 597 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9784 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7625779E-10 5.0229143E-10 midg,1,midg; midg,igrid,midg 5.4181115E-10 2.5757124E-10 1,midg,midg; igrid,midg,midg 5.7083382E-10 2.9665481E-10 gauss-seidel spectral radius is 0.9818047 estimated iterations to convergence 61 setup time was (sec) 0.4600000 now iterating at: 07:59:37 rms-change max change #iterations 7.8668274E-02 14.35015 at 10iterations 4.9239174E-03 0.7222366 at 20iterations 4.6347769E-04 5.7545245E-02 at 30iterations 1.1465394E-04 1.2674332E-02 at 40iterations 4.1298310E-05 4.4798851E-03 at 50iterations finished qdiffx linear iterations at : 07:59:40 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.1298310E-05 4.4798851E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 07:59:40 3.451u 0.170s 0:03.95 91.6% 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 Tue Oct 11 2011 at 07:59:40 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4030 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 1.592913 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 1.592913 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3877 net assigned charge : 12.15902 assigned positive charge : 620.4102 centred at (gu) : 87.80003 91.06629 87.99696 assigned negative charge : -608.2543 centred at (gu) : 87.83659 91.17154 87.89275 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 82057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 24359 mr = 55178 m= 2325 mr = 15884 m= 51 mr = 923 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 36808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 511 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 29440 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) : 0.5309708 object centre at (A) : -35.06550 169.8715 78.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0121899E-02 1.4728006E-02 midg,1,midg; midg,igrid,midg 1.0586335E-02 -6.0963440E-03 1,midg,midg; igrid,midg,midg 1.3424810E-02 9.1498913E-03 gauss-seidel spectral radius is 0.9982074 estimated iterations to convergence 188 setup time was (sec) 0.6200000 now iterating at: 07:59:41 rms-change max change #iterations 3.790239 164.4893 at 10iterations 1.585235 53.92907 at 20iterations 0.6671631 21.06012 at 30iterations 0.2806541 10.02430 at 40iterations 0.1179375 4.275272 at 50iterations 4.9799222E-02 1.661610 at 60iterations 2.0863812E-02 0.6430166 at 70iterations 8.7991394E-03 0.2920332 at 80iterations 3.7058762E-03 0.1231162 at 90iterations 1.5736313E-03 5.0918579E-02 at 100iterations 6.6568755E-04 2.0910263E-02 at 110iterations 2.8566460E-04 1.0178089E-02 at 120iterations finished qdiffx linear iterations at : 07:59:48 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.8566460E-04 1.0178089E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 07:59:49 7.804u 0.191s 0:08.55 93.4% 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 Tue Oct 11 2011 at 07:59:49 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4030 !!! WARNING: SEP 202 has a net charge of -0.4750 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: ASN 1035 has a net charge of -0.2720 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: 2.389369 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): -64.14800 -5.983000 ymin,ymax (A): 136.3480 203.3950 zmin,zma (A): 49.32400 108.2380 x,y,z range (A): 58.16500 67.04700 58.91400 scale (grids/A): 2.389369 object centre (A): -35.06550 169.8715 78.78100 number of atom coordinates read : 4030 total number of charged atoms : 3877 net assigned charge : 12.15902 assigned positive charge : 620.4102 centred at (gu) : 86.69974 91.59921 86.99541 assigned negative charge : -608.2543 centred at (gu) : 86.75478 91.75715 86.83902 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 190256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37299 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 86363 mr = 135100 m= 22877 mr = 66671 m= 3347 mr = 16214 m= 181 mr = 1881 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 83119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 30942 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) : 1.592913 object centre at (A) : -35.06550 169.8715 78.78100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1393370 0.2194644 midg,1,midg; midg,igrid,midg 5.6951609E-02 -5.2578714E-02 1,midg,midg; igrid,midg,midg 0.1900538 0.1288524 gauss-seidel spectral radius is 0.9991854 estimated iterations to convergence 277 setup time was (sec) 1.230000 now iterating at: 07:59:50 rms-change max change #iterations 10.17421 271.9323 at 10iterations 5.951424 145.1598 at 20iterations 3.432023 84.91042 at 30iterations 1.970178 40.89915 at 40iterations 1.129758 25.59446 at 50iterations 0.6437491 13.63390 at 60iterations 0.3655376 7.726670 at 70iterations 0.2071704 4.304642 at 80iterations 0.1170850 2.424812 at 90iterations 6.6286460E-02 1.349667 at 100iterations 3.7355777E-02 0.7366240 at 110iterations 2.1042675E-02 0.4385741 at 120iterations 1.1866177E-02 0.2251282 at 130iterations 6.6818479E-03 0.1409674 at 140iterations 3.7533147E-03 7.8504562E-02 at 150iterations 2.1099676E-03 4.4795990E-02 at 160iterations 1.1881859E-03 2.2563934E-02 at 170iterations 6.6780625E-04 1.2326968E-02 at 180iterations finished qdiffx linear iterations at : 08:00:02 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 6.6780625E-04 1.2326968E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 08:00:02 12.736u 0.210s 0:13.41 96.4% 0+0k 0+0io 0pf+0w