Sun Oct 9 12:40:17 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 12:40:17 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 0.6790524 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): -5.595000 43.91800 ymin,ymax (A): -14.27700 38.14900 zmin,zma (A): 2.815000 45.41000 x,y,z range (A): 49.51300 52.42600 42.59500 scale (grids/A): 0.6790524 object centre (A): 19.16150 11.93600 24.11250 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 363.6292 centred at (gu) : 89.35011 90.58019 90.19784 assigned negative charge : -361.1295 centred at (gu) : 89.36664 90.77467 90.26712 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7330 nv = 96 ne = 84 npr = 48314 no. pairs analyzed = 48314 no. exposed pairs = 2917 no. arc points = 20754 no. surface atoms = 982 nbur = 1394 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4023 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2014 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0053474E-08 -1.0126317E-08 midg,1,midg; midg,igrid,midg 5.9787453E-08 -5.3958452E-08 1,midg,midg; igrid,midg,midg 1.8019740E-08 5.3569282E-09 gauss-seidel spectral radius is 0.9887338 estimated iterations to convergence 77 setup time was (sec) 0.6000000 now iterating at: 12:40:18 rms-change max change #iterations 0.1828267 30.36788 at 10iterations 2.1208374E-02 3.229813 at 20iterations 2.8647031E-03 0.4183426 at 30iterations 5.8831961E-04 9.8388672E-02 at 40iterations 1.7249101E-04 3.0460358E-02 at 50iterations finished qdiffx linear iterations at : 12:40:21 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 1.7249101E-04 3.0460358E-02 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 12:40:21 4.048u 0.263s 0:04.58 93.8% 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 12:40:21 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 2.037157 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): -5.595000 43.91800 ymin,ymax (A): -14.27700 38.14900 zmin,zma (A): 2.815000 45.41000 x,y,z range (A): 49.51300 52.42600 42.59500 scale (grids/A): 2.037157 object centre (A): 19.16150 11.93600 24.11250 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 363.6292 centred at (gu) : 88.04994 91.74006 90.59331 assigned negative charge : -361.1295 centred at (gu) : 88.09968 92.32378 90.80108 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78176 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20754 grid for indexing accessible points = 1.400000 m= 29298 mr = 54332 m= 4884 mr = 21439 m= 343 mr = 3043 m= 6 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 33732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 17683 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) : 0.6790524 object centre at (A) : 19.16150 11.93600 24.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6377543E-02 1.0559307E-02 midg,1,midg; midg,igrid,midg 1.5821792E-02 -6.5291934E-02 1,midg,midg; igrid,midg,midg 3.7112836E-02 -1.3902288E-02 gauss-seidel spectral radius is 0.9987804 estimated iterations to convergence 227 setup time was (sec) 1.010000 now iterating at: 12:40:23 rms-change max change #iterations 4.628292 192.2921 at 10iterations 2.246749 71.32115 at 20iterations 1.094104 31.84467 at 30iterations 0.5355688 15.90112 at 40iterations 0.2610483 8.887726 at 50iterations 0.1276967 3.983380 at 60iterations 6.2501870E-02 1.952272 at 70iterations 3.0495536E-02 0.9676247 at 80iterations 1.5110624E-02 0.4291725 at 90iterations 7.4975137E-03 0.2414703 at 100iterations 3.7811634E-03 0.1193695 at 110iterations 1.9630520E-03 5.8601379E-02 at 120iterations finished qdiffx linear iterations at : 12:40:31 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 1.9630520E-03 5.8601379E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 12:40:32 9.494u 0.283s 0:10.03 97.4% 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 12:40:32 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 3.055736 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): -5.595000 43.91800 ymin,ymax (A): -14.27700 38.14900 zmin,zma (A): 2.815000 45.41000 x,y,z range (A): 49.51300 52.42600 42.59500 scale (grids/A): 3.055736 object centre (A): 19.16150 11.93600 24.11250 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500025 assigned positive charge : 363.6292 centred at (gu) : 87.07482 92.60992 90.88980 assigned negative charge : -361.1295 centred at (gu) : 87.14943 93.48563 91.20158 start vw surface at 0.1600000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 180084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20754 grid for indexing accessible points = 1.400000 m= 93568 mr = 130957 m= 35045 mr = 76598 m= 8870 mr = 27992 m= 1518 mr = 6605 m= 135 mr = 1010 m= 0 mr = 72 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 75986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 17867 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) : 2.037157 object centre at (A) : 19.16150 11.93600 24.11250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4258949 1.9584162E-02 midg,1,midg; midg,igrid,midg 0.4482188 -0.7058280 1,midg,midg; igrid,midg,midg 0.4078080 -0.3242584 gauss-seidel spectral radius is 0.9992862 estimated iterations to convergence 295 setup time was (sec) 2.180000 now iterating at: 12:40:34 rms-change max change #iterations 10.60644 432.5767 at 10iterations 6.257205 151.6865 at 20iterations 3.684161 94.84195 at 30iterations 2.163107 46.00853 at 40iterations 1.268237 25.24524 at 50iterations 0.7423913 12.03392 at 60iterations 0.4334157 7.888638 at 70iterations 0.2530704 4.905560 at 80iterations 0.1478029 2.607128 at 90iterations 8.6233206E-02 1.668381 at 100iterations 5.0356951E-02 0.8615084 at 110iterations 2.9495183E-02 0.5004082 at 120iterations 1.7395714E-02 0.3244286 at 130iterations 1.0407722E-02 0.1869354 at 140iterations 6.3568386E-03 0.1212921 at 150iterations 4.0251580E-03 8.0013275E-02 at 160iterations 2.6887322E-03 6.0340881E-02 at 170iterations 1.8998232E-03 4.1900635E-02 at 180iterations finished qdiffx linear iterations at : 12:40:48 total time elapsed so far: 15.87000 # loops : 180 mean,max change (kT/e) : 1.8998232E-03 4.1900635E-02 energy calculations done at 15.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.05000 DelPhi exited at 12:40:48 16.052u 0.291s 0:16.62 98.3% 0+0k 0+0io 0pf+0w