Tue Oct 11 08:06:39 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 Tue Oct 11 2011 at 08:06:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5649628 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 0.5649628 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 360.5552 centred at (gu) : 90.03565 88.58273 91.59673 assigned negative charge : -353.5558 centred at (gu) : 89.91122 88.64880 91.55988 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 4965 nv = 96 ne = 84 npr = 48023 no. pairs analyzed = 48023 no. exposed pairs = 3198 no. arc points = 22632 no. surface atoms = 1072 nbur = 1320 mkacc time = 0.1400000 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 = 1.540000 m= 221 mr = 2426 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3600000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4151110E-10 1.8364348E-09 midg,1,midg; midg,igrid,midg 2.1861062E-09 1.3593042E-10 1,midg,midg; igrid,midg,midg -4.4309834E-10 2.1711943E-09 gauss-seidel spectral radius is 0.9837912 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 08:06:40 rms-change max change #iterations 7.4049957E-02 13.51448 at 10iterations 5.7823211E-03 0.9628706 at 20iterations 7.1239489E-04 0.1736488 at 30iterations 1.8380162E-04 4.9533844E-02 at 40iterations 5.5796820E-05 1.5110016E-02 at 50iterations finished qdiffx linear iterations at : 08:06:43 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 5.5796820E-05 1.5110016E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 08:06:43 4.096u 0.152s 0:04.55 93.1% 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 Tue Oct 11 2011 at 08:06:43 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 = 2392 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.694888 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 1.694888 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 360.5552 centred at (gu) : 90.10649 85.74798 94.78967 assigned negative charge : -353.5558 centred at (gu) : 89.73347 85.94634 94.67935 start vw surface at 0.2000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 54858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22632 grid for indexing accessible points = 1.400000 m= 16698 mr = 36013 m= 1881 mr = 11195 m= 64 mr = 914 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 25374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 261 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17379 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) : 0.5649628 object centre at (A) : 3.165000 48.51650 26.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9384028E-04 1.3526717E-02 midg,1,midg; midg,igrid,midg 4.1582566E-02 2.3675719E-02 1,midg,midg; igrid,midg,midg -7.0128995E-03 1.0870794E-02 gauss-seidel spectral radius is 0.9982550 estimated iterations to convergence 190 setup time was (sec) 0.8800000 now iterating at: 08:06:44 rms-change max change #iterations 3.186776 171.9340 at 10iterations 1.340077 52.94579 at 20iterations 0.5669712 23.04912 at 30iterations 0.2395159 8.860221 at 40iterations 0.1014637 3.681618 at 50iterations 4.3072075E-02 1.603350 at 60iterations 1.8368335E-02 0.6708679 at 70iterations 7.9020429E-03 0.3017292 at 80iterations 3.4774952E-03 0.1589088 at 90iterations 1.6045816E-03 6.8042755E-02 at 100iterations 8.0972043E-04 4.1939735E-02 at 110iterations 4.6013560E-04 2.6206970E-02 at 120iterations finished qdiffx linear iterations at : 08:06:52 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 4.6013560E-04 2.6206970E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.840000 DelPhi exited at 08:06:53 8.840u 0.230s 0:09.72 93.3% 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 Tue Oct 11 2011 at 08:06:53 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 = 2392 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: 2.542332 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): -19.09200 25.42200 ymin,ymax (A): 17.01000 80.02300 zmin,zma (A): 2.263000 51.62300 x,y,z range (A): 44.51400 63.01300 49.36000 scale (grids/A): 2.542332 object centre (A): 3.165000 48.51650 26.94300 number of atom coordinates read : 2392 total number of charged atoms : 2254 net assigned charge : 7.000014 assigned positive charge : 360.5552 centred at (gu) : 90.15955 83.62195 97.18448 assigned negative charge : -353.5558 centred at (gu) : 89.60020 83.91949 97.01890 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 127374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22632 grid for indexing accessible points = 1.400000 m= 57059 mr = 88648 m= 16652 mr = 44272 m= 2896 mr = 12135 m= 253 mr = 1857 m= 6 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 57205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18022 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) : 1.694888 object centre at (A) : 3.165000 48.51650 26.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9489789E-03 0.1818183 midg,1,midg; midg,igrid,midg 0.6123095 0.3820466 1,midg,midg; igrid,midg,midg -9.4303437E-02 0.1411774 gauss-seidel spectral radius is 0.9991481 estimated iterations to convergence 271 setup time was (sec) 1.570000 now iterating at: 08:06:55 rms-change max change #iterations 8.177005 329.8690 at 10iterations 4.612070 123.7851 at 20iterations 2.586621 68.66972 at 30iterations 1.446776 39.95533 at 40iterations 0.8083020 21.34851 at 50iterations 0.4490668 11.31314 at 60iterations 0.2492715 5.984550 at 70iterations 0.1383592 3.030251 at 80iterations 7.6564394E-02 1.996692 at 90iterations 4.2450797E-02 1.104656 at 100iterations 2.3442207E-02 0.5505981 at 110iterations 1.3029455E-02 0.2895374 at 120iterations 7.2689904E-03 0.1792774 at 130iterations 4.0842835E-03 0.1131554 at 140iterations 2.3357517E-03 5.8311462E-02 at 150iterations 1.3830549E-03 3.9875031E-02 at 160iterations 8.5575535E-04 2.4433136E-02 at 170iterations 5.6783843E-04 1.7070770E-02 at 180iterations finished qdiffx linear iterations at : 08:07:07 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 5.6783843E-04 1.7070770E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 08:07:08 13.942u 0.209s 0:14.56 97.1% 0+0k 0+0io 0pf+0w