Sun Oct 9 07:44:58 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 Sun Oct 9 2011 at 07:44:59 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 has a net charge of -2.0000 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: 0.6940113 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 0.6940113 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 253.3412 centred at (gu) : 89.63000 91.12615 90.05889 assigned negative charge : -263.8411 centred at (gu) : 89.75615 90.83228 89.82232 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5488 nv = 96 ne = 84 npr = 36701 no. pairs analyzed = 36701 no. exposed pairs = 2083 no. arc points = 14542 no. surface atoms = 712 nbur = 987 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 256 mr = 3062 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.2200000 number of dielectric boundary points 2642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1277 ## 108 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6152 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3815317E-07 6.1471952E-09 midg,1,midg; midg,igrid,midg -1.2685172E-07 2.9694764E-08 1,midg,midg; igrid,midg,midg -2.8545472E-08 -9.7188632E-08 gauss-seidel spectral radius is 0.9891466 estimated iterations to convergence 78 setup time was (sec) 0.4300000 now iterating at: 07:44:59 rms-change max change #iterations 0.1754201 32.18117 at 10iterations 2.0441610E-02 3.426479 at 20iterations 2.4297929E-03 0.3597221 at 30iterations 2.8008729E-04 4.9736023E-02 at 40iterations 3.3167726E-05 5.6762695E-03 at 50iterations finished qdiffx linear iterations at : 07:45:02 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 3.3167726E-05 5.6762695E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 07:45:02 3.025u 0.150s 0:03.45 91.8% 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 Sun Oct 9 2011 at 07:45:02 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 has a net charge of -2.0000 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: 2.082034 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 2.082034 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 253.3412 centred at (gu) : 88.89001 93.37862 90.17671 assigned negative charge : -263.8411 centred at (gu) : 89.26850 92.49688 89.46684 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14542 grid for indexing accessible points = 1.400000 m= 21328 mr = 40853 m= 3349 mr = 16169 m= 223 mr = 2218 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2957 time to turn everything in is 0.4300000 number of dielectric boundary points 24255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12401 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) : 0.6940113 object centre at (A) : 26.98950 0.1464996 -16.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2896029E-02 -9.8335370E-03 midg,1,midg; midg,igrid,midg -4.5719218E-02 3.5593063E-02 1,midg,midg; igrid,midg,midg -2.4520848E-02 -6.8432152E-02 gauss-seidel spectral radius is 0.9987513 estimated iterations to convergence 224 setup time was (sec) 0.7000000 now iterating at: 07:45:03 rms-change max change #iterations 4.079107 173.7085 at 10iterations 1.974476 72.23917 at 20iterations 0.9541917 33.06070 at 30iterations 0.4627581 15.61430 at 40iterations 0.2246893 7.649485 at 50iterations 0.1088356 3.618622 at 60iterations 5.2541733E-02 1.780112 at 70iterations 2.5419397E-02 0.9273701 at 80iterations 1.2287216E-02 0.4730635 at 90iterations 5.9292247E-03 0.2283363 at 100iterations 2.8851328E-03 9.4160080E-02 at 110iterations 1.3902113E-03 5.2047729E-02 at 120iterations finished qdiffx linear iterations at : 07:45:09 total time elapsed so far: 6.600000 # loops : 120 mean,max change (kT/e) : 1.3902113E-03 5.2047729E-02 energy calculations done at 6.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 07:45:09 6.759u 0.168s 0:07.20 95.9% 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 Sun Oct 9 2011 at 07:45:09 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1699 !!! WARNING: NAP 202 has a net charge of -2.0000 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: 3.123051 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): 5.338000 48.64100 ymin,ymax (A): -21.23900 21.53200 zmin,zma (A): -41.99300 9.302999 x,y,z range (A): 43.30300 42.77100 51.29600 scale (grids/A): 3.123051 object centre (A): 26.98950 0.1464996 -16.34500 number of atom coordinates read : 1699 total number of charged atoms : 1562 net assigned charge : -10.49999 assigned positive charge : 253.3412 centred at (gu) : 88.33498 95.06792 90.26509 assigned negative charge : -263.8411 centred at (gu) : 88.90277 93.74551 89.20032 start vw surface at 0.1200000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 135566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14542 grid for indexing accessible points = 1.400000 m= 68912 mr = 98661 m= 25188 mr = 57300 m= 6221 mr = 20857 m= 1082 mr = 4769 m= 67 mr = 798 m= 0 mr = 20 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 9428 time to turn everything in is 1.310000 number of dielectric boundary points 54631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 12496 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) : 2.082034 object centre at (A) : 26.98950 0.1464996 -16.34500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8290272 0.1014473 midg,1,midg; midg,igrid,midg -0.3502845 0.3931875 1,midg,midg; igrid,midg,midg -0.1579104 -0.7589293 gauss-seidel spectral radius is 0.9992681 estimated iterations to convergence 292 setup time was (sec) 1.590000 now iterating at: 07:45:11 rms-change max change #iterations 9.204663 402.2943 at 10iterations 5.278769 119.1847 at 20iterations 3.032338 62.24915 at 30iterations 1.742149 31.94139 at 40iterations 1.000422 20.26347 at 50iterations 0.5759577 11.67921 at 60iterations 0.3308427 6.631611 at 70iterations 0.1900658 3.877274 at 80iterations 0.1093601 2.086584 at 90iterations 6.2928326E-02 1.248506 at 100iterations 3.6057841E-02 0.7368641 at 110iterations 2.0762278E-02 0.4215145 at 120iterations 1.1949502E-02 0.2283931 at 130iterations 6.8811104E-03 0.1319809 at 140iterations 3.9541773E-03 8.0115080E-02 at 150iterations 2.2764830E-03 4.2519569E-02 at 160iterations 1.3079608E-03 2.4290085E-02 at 170iterations 7.5313175E-04 1.4426589E-02 at 180iterations finished qdiffx linear iterations at : 07:45:20 total time elapsed so far: 10.79000 # loops : 180 mean,max change (kT/e) : 7.5313175E-04 1.4426589E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 07:45:21 10.966u 0.170s 0:11.40 97.6% 0+0k 0+0io 0pf+0w