Tue Oct 11 03:17:11 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 03:17:11 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: NAI 1721 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5344383 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): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 0.5344383 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.500012 assigned positive charge : 785.0409 centred at (gu) : 89.39825 89.97424 90.27268 assigned negative charge : -782.5472 centred at (gu) : 89.41966 89.90652 90.26071 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 9125 nv = 96 ne = 84 npr = 102364 no. pairs analyzed = 102364 no. exposed pairs = 5988 no. arc points = 40943 no. surface atoms = 2010 nbur = 3051 mkacc time = 0.2400000 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 = 1.596000 m= 345 mr = 5061 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 79 time to turn everything in is 0.5500000 number of dielectric boundary points 4398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4069 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 12297 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4748875E-12 2.0014713E-10 midg,1,midg; midg,igrid,midg -4.2029755E-10 5.9851196E-10 1,midg,midg; igrid,midg,midg 3.0016772E-10 -5.4956803E-11 gauss-seidel spectral radius is 0.9821065 estimated iterations to convergence 62 setup time was (sec) 0.8000000 now iterating at: 03:17:13 rms-change max change #iterations 9.1925368E-02 12.03577 at 10iterations 6.2014549E-03 0.8103409 at 20iterations 7.1338302E-04 9.0244293E-02 at 30iterations 2.0810944E-04 2.6733398E-02 at 40iterations 7.1486764E-05 9.4537735E-03 at 50iterations finished qdiffx linear iterations at : 03:17:15 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 7.1486764E-05 9.4537735E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.780000 DelPhi exited at 03:17:16 3.783u 0.175s 0:04.65 84.9% 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 Tue Oct 11 2011 at 03:17:16 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: NAI 1721 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.603315 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): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 1.603315 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.500012 assigned positive charge : 785.0409 centred at (gu) : 88.19297 89.92065 90.81613 assigned negative charge : -782.5472 centred at (gu) : 88.25881 89.71932 90.78178 start vw surface at 0.2300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 103051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40943 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 32430 mr = 73038 m= 3078 mr = 23080 m= 63 mr = 1417 m= 0 mr = 2 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3995 time to turn everything in is 0.7800000 number of dielectric boundary points 41085 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 387 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 37704 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) : 0.5344383 object centre at (A) : 48.71350 33.15200 37.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7800670E-02 2.0691063E-02 midg,1,midg; midg,igrid,midg -1.7712275E-02 -5.8664493E-03 1,midg,midg; igrid,midg,midg 4.1251071E-03 -6.1689125E-04 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 1.080000 now iterating at: 03:17:18 rms-change max change #iterations 4.460923 161.2922 at 10iterations 1.923215 57.89383 at 20iterations 0.8303674 29.41049 at 30iterations 0.3580761 10.06921 at 40iterations 0.1542760 4.325077 at 50iterations 6.6742472E-02 1.972575 at 60iterations 2.8769460E-02 0.8335419 at 70iterations 1.2486711E-02 0.3581133 at 80iterations 5.4384959E-03 0.1764793 at 90iterations 2.3842584E-03 6.6865921E-02 at 100iterations 1.0709174E-03 3.2926559E-02 at 110iterations 4.9901678E-04 1.5069962E-02 at 120iterations finished qdiffx linear iterations at : 03:17:25 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 4.9901678E-04 1.5069962E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 03:17:25 8.236u 0.261s 0:09.25 91.7% 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 Tue Oct 11 2011 at 03:17:25 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5061 !!! WARNING: NAI 1721 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.404972 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): 17.30500 80.12200 ymin,ymax (A): -0.1539999 66.45800 zmin,zma (A): 6.617000 69.29200 x,y,z range (A): 62.81700 66.61200 62.67500 scale (grids/A): 2.404972 object centre (A): 48.71350 33.15200 37.95450 number of atom coordinates read : 5061 total number of charged atoms : 4952 net assigned charge : 2.500012 assigned positive charge : 785.0409 centred at (gu) : 87.28886 89.88050 91.22384 assigned negative charge : -782.5472 centred at (gu) : 87.38796 89.57870 91.17258 start vw surface at 0.2500000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 239731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40943 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 114313 mr = 178310 m= 31569 mr = 92496 m= 4450 mr = 24102 m= 259 mr = 2799 m= 3 mr = 83 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 13746 time to turn everything in is 1.820000 number of dielectric boundary points 92536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 39548 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) : 1.603315 object centre at (A) : 48.71350 33.15200 37.95450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2214149 0.3006640 midg,1,midg; midg,igrid,midg -0.1649365 -0.1755998 1,midg,midg; igrid,midg,midg -1.0520214E-02 -3.3425763E-02 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.150000 now iterating at: 03:17:28 rms-change max change #iterations 11.51920 312.8149 at 10iterations 6.714148 157.9572 at 20iterations 3.890355 75.18005 at 30iterations 2.245830 49.79427 at 40iterations 1.294455 23.84764 at 50iterations 0.7425326 14.96524 at 60iterations 0.4241783 7.426437 at 70iterations 0.2423206 4.802710 at 80iterations 0.1385882 2.316952 at 90iterations 7.9037018E-02 1.365092 at 100iterations 4.5139119E-02 0.8600798 at 110iterations 2.5672182E-02 0.4470139 at 120iterations 1.4657724E-02 0.2387710 at 130iterations 8.3634453E-03 0.1491529 at 140iterations 4.7815554E-03 7.6938629E-02 at 150iterations 2.7428106E-03 5.0682068E-02 at 160iterations 1.5831141E-03 2.8354645E-02 at 170iterations 9.2494523E-04 1.5777588E-02 at 180iterations finished qdiffx linear iterations at : 03:17:39 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 9.2494523E-04 1.5777588E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 03:17:39 13.054u 0.191s 0:13.56 97.6% 0+0k 0+0io 0pf+0w