Wed Feb 15 08:56:05 PST 2012 #!/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+sph_thinner.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 = amb.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 Wed Feb 15 2012 at 08:56:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 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: 0.5660588 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 0.5660588 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.499972 assigned positive charge : 411.0404 centred at (gu) : 90.13657 90.33788 89.72926 assigned negative charge : -412.5414 centred at (gu) : 90.13963 90.23607 89.68598 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5780 nv = 96 ne = 84 npr = 55517 no. pairs analyzed = 55517 no. exposed pairs = 3693 no. arc points = 26108 no. surface atoms = 1246 nbur = 1512 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= 281 mr = 2935 m= 1 mr = 8 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 3119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2616 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0703205E-10 3.2351968E-10 midg,1,midg; midg,igrid,midg -1.3958421E-09 1.1721549E-09 1,midg,midg; igrid,midg,midg -1.5796732E-10 -2.4891356E-10 gauss-seidel spectral radius is 0.9838829 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 08:56:06 rms-change max change #iterations 8.2299292E-02 18.43628 at 10iterations 5.9526558E-03 1.102977 at 20iterations 4.4597915E-04 7.9897404E-02 at 30iterations 3.3192151E-05 5.2156448E-03 at 40iterations 2.4350065E-06 4.2915344E-04 at 50iterations finished qdiffx linear iterations at : 08:56:09 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.4350065E-06 4.2915344E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 08:56:10 3.694u 0.170s 0:04.38 88.1% 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 Wed Feb 15 2012 at 08:56:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.698176 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 1.698176 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.499972 assigned positive charge : 411.0404 centred at (gu) : 90.40918 91.01292 89.18693 assigned negative charge : -412.5414 centred at (gu) : 90.41852 90.70779 89.05768 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 63719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26108 grid for indexing accessible points = 1.400000 m= 19539 mr = 42378 m= 2091 mr = 13183 m= 65 mr = 984 m= 0 mr = 6 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.5900000 number of dielectric boundary points 28863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20230 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) : 0.5660588 object centre at (A) : 1.259500 1.532500 16.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5920722E-03 -1.7303887E-03 midg,1,midg; midg,igrid,midg -1.6435718E-02 7.6951711E-03 1,midg,midg; igrid,midg,midg 5.1358892E-03 1.9254616E-02 gauss-seidel spectral radius is 0.9983035 estimated iterations to convergence 193 setup time was (sec) 0.9000000 now iterating at: 08:56:12 rms-change max change #iterations 3.473943 188.3695 at 10iterations 1.484483 53.37743 at 20iterations 0.6364589 22.46611 at 30iterations 0.2735533 10.71505 at 40iterations 0.1167930 4.293199 at 50iterations 5.0295889E-02 1.890396 at 60iterations 2.1572718E-02 0.7226782 at 70iterations 9.2450408E-03 0.3182046 at 80iterations 3.9734356E-03 0.1457767 at 90iterations 1.7030471E-03 5.9024811E-02 at 100iterations 7.2991732E-04 2.7682781E-02 at 110iterations 3.1469567E-04 1.2087822E-02 at 120iterations finished qdiffx linear iterations at : 08:56:18 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 3.1469567E-04 1.2087822E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:56:20 7.771u 0.241s 0:09.08 88.2% 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 Wed Feb 15 2012 at 08:56:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 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: 2.547264 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 2.547264 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.499972 assigned positive charge : 411.0404 centred at (gu) : 90.61362 91.51926 88.78017 assigned negative charge : -412.5414 centred at (gu) : 90.62775 91.06160 88.58643 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 147779 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26108 grid for indexing accessible points = 1.400000 m= 67546 mr = 103932 m= 19325 mr = 52700 m= 3244 mr = 14225 m= 248 mr = 2047 m= 6 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 1.150000 number of dielectric boundary points 65130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20942 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) : 1.698176 object centre at (A) : 1.259500 1.532500 16.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2981330E-02 -4.2480513E-02 midg,1,midg; midg,igrid,midg -0.2056939 0.1377130 1,midg,midg; igrid,midg,midg 0.2572904 0.3503461 gauss-seidel spectral radius is 0.9991744 estimated iterations to convergence 275 setup time was (sec) 1.450000 now iterating at: 08:56:21 rms-change max change #iterations 8.805400 303.3528 at 10iterations 5.008787 123.3541 at 20iterations 2.839509 66.57613 at 30iterations 1.601599 39.45294 at 40iterations 0.8979952 19.64886 at 50iterations 0.5042838 12.30204 at 60iterations 0.2821053 6.302277 at 70iterations 0.1573748 3.286315 at 80iterations 8.7502375E-02 1.939781 at 90iterations 4.8895329E-02 1.036859 at 100iterations 2.7228575E-02 0.5713921 at 110iterations 1.5118596E-02 0.3490067 at 120iterations 8.4265796E-03 0.1771163 at 130iterations 4.6839938E-03 9.7667694E-02 at 140iterations 2.6055828E-03 5.2556992E-02 at 150iterations 1.4444970E-03 2.9935837E-02 at 160iterations 8.0542610E-04 1.6328812E-02 at 170iterations 4.4720914E-04 8.7738037E-03 at 180iterations finished qdiffx linear iterations at : 08:56:32 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 4.4720914E-04 8.7738037E-03 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 08:56:33 12.480u 0.181s 0:13.23 95.6% 0+0k 0+0io 0pf+0w