Sat Oct 8 11:44:59 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 Sat Oct 8 2011 at 11:44:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 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: 0.6265289 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 0.6265289 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.999992 assigned positive charge : 394.7450 centred at (gu) : 91.47484 91.26511 91.40385 assigned negative charge : -396.7455 centred at (gu) : 91.52384 91.15541 91.44058 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6578 nv = 96 ne = 84 npr = 52733 no. pairs analyzed = 52733 no. exposed pairs = 3156 no. arc points = 22899 no. surface atoms = 1063 nbur = 1523 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 3493 m= 5 mr = 48 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 0.3300000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2300 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2768186E-10 -6.7530470E-09 midg,1,midg; midg,igrid,midg -8.3412148E-09 9.1603054E-09 1,midg,midg; igrid,midg,midg 1.4305972E-09 -8.2655012E-09 gauss-seidel spectral radius is 0.9868040 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 11:45:00 rms-change max change #iterations 0.1328691 20.95211 at 10iterations 1.2331706E-02 1.764931 at 20iterations 1.1618787E-03 0.1677094 at 30iterations 1.0862288E-04 1.7537355E-02 at 40iterations 1.0260503E-05 1.4076233E-03 at 50iterations finished qdiffx linear iterations at : 11:45:04 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.0260503E-05 1.4076233E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 11:45:04 4.112u 0.285s 0:04.68 93.8% 0+0k 0+0io 6pf+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 11:45:04 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 = 2586 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: 1.879587 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 1.879587 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.999992 assigned positive charge : 394.7450 centred at (gu) : 94.42426 93.79487 94.21093 assigned negative charge : -396.7455 centred at (gu) : 94.57135 93.46597 94.32177 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71776 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22899 grid for indexing accessible points = 1.400000 m= 24100 mr = 48598 m= 3503 mr = 17368 m= 211 mr = 2124 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 802 time to turn everything in is 0.6500000 number of dielectric boundary points 31426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19183 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) : 0.6265289 object centre at (A) : 44.30450 38.45800 42.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3626595E-04 -1.8836750E-02 midg,1,midg; midg,igrid,midg -1.0984655E-02 -3.7959885E-04 1,midg,midg; igrid,midg,midg 1.4982504E-02 -3.4806203E-02 gauss-seidel spectral radius is 0.9985969 estimated iterations to convergence 212 setup time was (sec) 0.9700000 now iterating at: 11:45:05 rms-change max change #iterations 4.156111 211.1333 at 10iterations 1.922322 74.25572 at 20iterations 0.8862622 28.75947 at 30iterations 0.4103976 14.94052 at 40iterations 0.1900117 6.258209 at 50iterations 8.7914646E-02 2.704309 at 60iterations 4.0649567E-02 1.269777 at 70iterations 1.8895609E-02 0.6527054 at 80iterations 8.7496405E-03 0.3042564 at 90iterations 4.0485230E-03 0.1285667 at 100iterations 1.8733841E-03 6.2550545E-02 at 110iterations 8.6938246E-04 3.0349731E-02 at 120iterations finished qdiffx linear iterations at : 11:45:14 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 8.6938246E-04 3.0349731E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 11:45:14 9.590u 0.293s 0:10.15 97.3% 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 11:45:14 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 = 2586 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: 2.819380 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): 15.89400 72.71500 ymin,ymax (A): 13.00700 63.90900 zmin,zma (A): 21.30200 64.63400 x,y,z range (A): 56.82100 50.90200 43.33200 scale (grids/A): 2.819380 object centre (A): 44.30450 38.45800 42.96800 number of atom coordinates read : 2586 total number of charged atoms : 2446 net assigned charge : -1.999992 assigned positive charge : 394.7450 centred at (gu) : 96.63625 95.69216 96.31634 assigned negative charge : -396.7455 centred at (gu) : 96.85698 95.19902 96.48256 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 166194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22899 grid for indexing accessible points = 1.400000 m= 79240 mr = 118334 m= 27098 mr = 63902 m= 6215 mr = 21420 m= 882 mr = 4632 m= 67 mr = 604 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2658 time to turn everything in is 1.620000 number of dielectric boundary points 70771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 19568 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) : 1.879587 object centre at (A) : 44.30450 38.45800 42.96800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9751899E-02 -0.3312939 midg,1,midg; midg,igrid,midg -9.7957596E-02 -7.5800434E-02 1,midg,midg; igrid,midg,midg 0.2472479 -0.2567588 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.950000 now iterating at: 11:45:17 rms-change max change #iterations 9.742049 347.9845 at 10iterations 5.657682 121.0533 at 20iterations 3.249916 64.48277 at 30iterations 1.859061 36.66684 at 40iterations 1.063611 18.73821 at 50iterations 0.6079492 11.15960 at 60iterations 0.3480027 7.148771 at 70iterations 0.1982412 4.015705 at 80iterations 0.1130570 2.077272 at 90iterations 6.4642511E-02 1.165632 at 100iterations 3.6902163E-02 0.7774649 at 110iterations 2.1091079E-02 0.4021626 at 120iterations 1.2027876E-02 0.2366257 at 130iterations 6.8573728E-03 0.1298838 at 140iterations 3.9142733E-03 7.5180054E-02 at 150iterations 2.2362769E-03 4.1238785E-02 at 160iterations 1.2770856E-03 2.5420189E-02 at 170iterations 7.2978809E-04 1.3406754E-02 at 180iterations finished qdiffx linear iterations at : 11:45:30 total time elapsed so far: 15.82000 # loops : 180 mean,max change (kT/e) : 7.2978809E-04 1.3406754E-02 energy calculations done at 15.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.99000 DelPhi exited at 11:45:31 15.992u 0.317s 0:16.60 98.1% 0+0k 0+0io 0pf+0w