Sat Oct 8 17:11:34 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 Sat Oct 8 2011 at 17:11:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 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: 0.5492471 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): 37.69500 92.64900 ymin,ymax (A): 15.61400 80.43000 zmin,zma (A): -21.62300 25.16400 x,y,z range (A): 54.95400 64.81600 46.78700 scale (grids/A): 0.5492471 object centre (A): 65.17200 48.02200 1.770500 number of atom coordinates read : 3276 total number of charged atoms : 3131 net assigned charge : -6.499980 assigned positive charge : 490.0009 centred at (gu) : 90.30943 90.44601 89.84744 assigned negative charge : -496.5020 centred at (gu) : 90.31307 90.41376 89.81411 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 66561 no. pairs analyzed = 66561 no. exposed pairs = 4118 no. arc points = 28325 no. surface atoms = 1392 nbur = 1884 mkacc time = 0.1500000 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= 254 mr = 3455 m= 2 mr = 14 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 0.3400000 number of dielectric boundary points 3280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2928 ## 409 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6927109E-10 -1.7615161E-10 midg,1,midg; midg,igrid,midg -6.5701622E-10 -2.1114475E-10 1,midg,midg; igrid,midg,midg -3.9950174E-10 -5.2898275E-10 gauss-seidel spectral radius is 0.9829277 estimated iterations to convergence 63 setup time was (sec) 0.6100000 now iterating at: 17:11:35 rms-change max change #iterations 8.1319742E-02 11.43414 at 10iterations 5.4080668E-03 1.100682 at 20iterations 3.7402613E-04 6.6953659E-02 at 30iterations 3.1837008E-05 4.0721893E-03 at 40iterations 6.0380580E-06 9.6130371E-04 at 50iterations finished qdiffx linear iterations at : 17:11:38 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 6.0380580E-06 9.6130371E-04 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 17:11:39 4.214u 0.234s 0:04.73 93.8% 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 Sat Oct 8 2011 at 17:11:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 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: 1.647741 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): 37.69500 92.64900 ymin,ymax (A): 15.61400 80.43000 zmin,zma (A): -21.62300 25.16400 x,y,z range (A): 54.95400 64.81600 46.78700 scale (grids/A): 1.647741 object centre (A): 65.17200 48.02200 1.770500 number of atom coordinates read : 3276 total number of charged atoms : 3131 net assigned charge : -6.499980 assigned positive charge : 490.0009 centred at (gu) : 90.92722 91.33764 89.54148 assigned negative charge : -496.5020 centred at (gu) : 90.93895 91.24077 89.44193 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71205 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28325 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23107 mr = 49227 m= 2554 mr = 16199 m= 73 mr = 1242 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.5400000 number of dielectric boundary points 30268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 293 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 24048 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) : 0.5492471 object centre at (A) : 65.17200 48.02200 1.770500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7341115E-03 -4.3218792E-03 midg,1,midg; midg,igrid,midg 8.0883512E-03 1.8497553E-02 1,midg,midg; igrid,midg,midg -1.4756233E-02 -6.6663167E-03 gauss-seidel spectral radius is 0.9982488 estimated iterations to convergence 190 setup time was (sec) 0.8800000 now iterating at: 17:11:40 rms-change max change #iterations 3.596171 165.3257 at 10iterations 1.521740 55.59958 at 20iterations 0.6445327 24.61445 at 30iterations 0.2735771 10.83167 at 40iterations 0.1159870 3.975549 at 50iterations 4.9324960E-02 1.665169 at 60iterations 2.0869644E-02 0.7124929 at 70iterations 8.8226562E-03 0.2924700 at 80iterations 3.7617965E-03 0.1269169 at 90iterations 1.6042567E-03 5.7200432E-02 at 100iterations 6.8407098E-04 2.2234917E-02 at 110iterations 2.9609035E-04 1.2023926E-02 at 120iterations finished qdiffx linear iterations at : 17:11:48 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.9609035E-04 1.2023926E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 17:11:49 9.490u 0.242s 0:10.03 97.0% 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 Sat Oct 8 2011 at 17:11:49 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3276 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: 2.471612 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): 37.69500 92.64900 ymin,ymax (A): 15.61400 80.43000 zmin,zma (A): -21.62300 25.16400 x,y,z range (A): 54.95400 64.81600 46.78700 scale (grids/A): 2.471612 object centre (A): 65.17200 48.02200 1.770500 number of atom coordinates read : 3276 total number of charged atoms : 3131 net assigned charge : -6.499980 assigned positive charge : 490.0009 centred at (gu) : 91.39066 92.00605 89.31207 assigned negative charge : -496.5020 centred at (gu) : 91.40819 91.86109 89.16260 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 165388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28325 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79150 mr = 120310 m= 23573 mr = 63165 m= 3994 mr = 17810 m= 287 mr = 2610 m= 5 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 150 time to turn everything in is 1.330000 number of dielectric boundary points 68385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 25030 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) : 1.647741 object centre at (A) : 65.17200 48.02200 1.770500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1063959 -3.8656212E-02 midg,1,midg; midg,igrid,midg 0.3316262 0.6053025 1,midg,midg; igrid,midg,midg -0.2274464 -5.5643119E-02 gauss-seidel spectral radius is 0.9991642 estimated iterations to convergence 273 setup time was (sec) 1.670000 now iterating at: 17:11:51 rms-change max change #iterations 9.210143 368.5812 at 10iterations 5.218411 122.2481 at 20iterations 2.948387 61.68700 at 30iterations 1.657363 34.78936 at 40iterations 0.9271379 20.90113 at 50iterations 0.5181920 10.05560 at 60iterations 0.2894918 6.738300 at 70iterations 0.1613760 3.228874 at 80iterations 8.9906976E-02 1.762065 at 90iterations 4.9850777E-02 0.9799747 at 100iterations 2.7677840E-02 0.5244178 at 110iterations 1.5436240E-02 0.3194580 at 120iterations 8.5572544E-03 0.1608772 at 130iterations 4.7703828E-03 8.9988708E-02 at 140iterations 2.6445182E-03 4.9026489E-02 at 150iterations 1.4703211E-03 2.9080495E-02 at 160iterations 8.1969419E-04 1.6645432E-02 at 170iterations 4.5617289E-04 8.6660385E-03 at 180iterations finished qdiffx linear iterations at : 17:12:04 total time elapsed so far: 14.99000 # loops : 180 mean,max change (kT/e) : 4.5617289E-04 8.6660385E-03 energy calculations done at 14.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.17000 DelPhi exited at 17:12:05 15.176u 0.267s 0:15.82 97.5% 0+0k 0+0io 0pf+0w