Sun Oct 9 07:57:02 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+sph.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 Sun Oct 9 2011 at 07:57:02 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 0.6927014 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 0.6927014 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499991 assigned positive charge : 336.1374 centred at (gu) : 90.01236 90.97151 89.80807 assigned negative charge : -339.6378 centred at (gu) : 90.03420 91.07583 89.90367 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7384 nv = 96 ne = 84 npr = 44197 no. pairs analyzed = 44197 no. exposed pairs = 2819 no. arc points = 20388 no. surface atoms = 944 nbur = 1271 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4079 m= 10 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.1900000 number of dielectric boundary points 3719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1899 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8191 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6813541E-08 -5.5240495E-08 midg,1,midg; midg,igrid,midg 1.5752912E-08 -7.3911856E-08 1,midg,midg; igrid,midg,midg -1.1870767E-08 -2.8763191E-08 gauss-seidel spectral radius is 0.9891645 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 07:57:03 rms-change max change #iterations 0.1932365 27.26496 at 10iterations 2.2904443E-02 2.989788 at 20iterations 2.6942363E-03 0.3899078 at 30iterations 3.1710268E-04 4.6013832E-02 at 40iterations 3.7169579E-05 5.2862167E-03 at 50iterations finished qdiffx linear iterations at : 07:57:06 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.7169579E-05 5.2862167E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:57:07 3.433u 0.556s 0:04.36 91.2% 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 Sun Oct 9 2011 at 07:57:07 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 2.078104 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 2.078104 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499991 assigned positive charge : 336.1374 centred at (gu) : 90.03693 92.91421 89.42377 assigned negative charge : -339.6378 centred at (gu) : 90.10246 93.22757 89.71103 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 77610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20388 grid for indexing accessible points = 1.400000 m= 30965 mr = 53341 m= 6442 mr = 23341 m= 605 mr = 4411 m= 23 mr = 282 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 451 time to turn everything in is 0.4400000 number of dielectric boundary points 34264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 16445 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) : 0.6927014 object centre at (A) : 27.43350 0.7275000 5.867001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7900638E-03 -3.5440996E-02 midg,1,midg; midg,igrid,midg 2.7986888E-02 -1.6683538E-02 1,midg,midg; igrid,midg,midg -1.4967703E-03 -3.1424999E-02 gauss-seidel spectral radius is 0.9988137 estimated iterations to convergence 230 setup time was (sec) 0.6700000 now iterating at: 07:57:08 rms-change max change #iterations 4.679674 178.3579 at 10iterations 2.292063 71.10496 at 20iterations 1.131195 36.97782 at 30iterations 0.5569578 15.95741 at 40iterations 0.2741226 9.036703 at 50iterations 0.1355109 4.213413 at 60iterations 6.6673622E-02 1.924196 at 70iterations 3.2920152E-02 1.059576 at 80iterations 1.6122418E-02 0.4646225 at 90iterations 7.9653440E-03 0.2769928 at 100iterations 3.9189714E-03 0.1244626 at 110iterations 1.9359995E-03 6.0743332E-02 at 120iterations finished qdiffx linear iterations at : 07:57:15 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.9359995E-03 6.0743332E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 07:57:15 8.007u 0.242s 0:08.70 94.7% 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 Sun Oct 9 2011 at 07:57:15 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2215 !!! WARNING: NDP 385 has a net charge of -3.0000 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: 3.117156 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): 4.651000 50.21600 ymin,ymax (A): -24.96900 26.42400 zmin,zma (A): -18.55900 30.29300 x,y,z range (A): 45.56500 51.39300 48.85200 scale (grids/A): 3.117156 object centre (A): 27.43350 0.7275000 5.867001 number of atom coordinates read : 2215 total number of charged atoms : 2073 net assigned charge : -3.499991 assigned positive charge : 336.1374 centred at (gu) : 90.05531 94.37129 89.13556 assigned negative charge : -339.6378 centred at (gu) : 90.15372 94.84144 89.56653 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 178571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20388 grid for indexing accessible points = 1.400000 m= 95281 mr = 128247 m= 40314 mr = 78720 m= 12197 mr = 33334 m= 2577 mr = 9563 m= 275 mr = 1864 m= 21 mr = 134 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 1.220000 number of dielectric boundary points 77364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 16584 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) : 2.078104 object centre at (A) : 27.43350 0.7275000 5.867001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1824826 -0.2740144 midg,1,midg; midg,igrid,midg 0.7975330 -6.0326178E-02 1,midg,midg; igrid,midg,midg -4.6437595E-02 -0.2996626 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.490000 now iterating at: 07:57:17 rms-change max change #iterations 10.51653 422.1224 at 10iterations 6.169646 122.8607 at 20iterations 3.602501 73.94582 at 30iterations 2.107678 49.06866 at 40iterations 1.234014 21.84066 at 50iterations 0.7197306 14.61769 at 60iterations 0.4207389 7.678192 at 70iterations 0.2450355 5.011536 at 80iterations 0.1427494 2.468677 at 90iterations 8.3404221E-02 1.390474 at 100iterations 4.8514418E-02 0.8655720 at 110iterations 2.8353248E-02 0.4713440 at 120iterations 1.6487479E-02 0.2787361 at 130iterations 9.6064201E-03 0.1670361 at 140iterations 5.6003495E-03 9.5685959E-02 at 150iterations 3.2650917E-03 5.8713913E-02 at 160iterations 1.9025195E-03 3.4051418E-02 at 170iterations 1.1121696E-03 1.8743277E-02 at 180iterations finished qdiffx linear iterations at : 07:57:29 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 1.1121696E-03 1.8743277E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 07:57:29 13.115u 0.292s 0:13.75 97.4% 0+0k 0+0io 0pf+0w