Sun Oct 9 07:59:54 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 Sun Oct 9 2011 at 07:59:54 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6929710 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 0.6929710 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499991 assigned positive charge : 333.7805 centred at (gu) : 90.09317 91.05311 90.11276 assigned negative charge : -337.2808 centred at (gu) : 90.11053 91.14236 90.21465 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7336 nv = 96 ne = 84 npr = 44211 no. pairs analyzed = 44211 no. exposed pairs = 2828 no. arc points = 20468 no. surface atoms = 939 nbur = 1265 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 3984 m= 1 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 76 time to turn everything in is 0.1800000 number of dielectric boundary points 3732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7978540E-08 -6.1221691E-08 midg,1,midg; midg,igrid,midg 1.0837029E-08 -6.7808891E-08 1,midg,midg; igrid,midg,midg -1.3420266E-08 -2.7488110E-08 gauss-seidel spectral radius is 0.9891717 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 07:59:54 rms-change max change #iterations 0.1907821 27.48509 at 10iterations 2.2427643E-02 2.957144 at 20iterations 2.6389915E-03 0.3449669 at 30iterations 3.0790627E-04 4.5870781E-02 at 40iterations 3.7043821E-05 5.1794052E-03 at 50iterations finished qdiffx linear iterations at : 07:59:57 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.7043821E-05 5.1794052E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 07:59:57 3.378u 0.174s 0:03.86 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 Sun Oct 9 2011 at 07:59:58 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.078913 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 2.078913 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499991 assigned positive charge : 333.7805 centred at (gu) : 90.27912 93.15897 90.33794 assigned negative charge : -337.2808 centred at (gu) : 90.33146 93.42692 90.64392 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 77544 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20468 grid for indexing accessible points = 1.400000 m= 30652 mr = 53019 m= 6123 mr = 23118 m= 602 mr = 4121 m= 23 mr = 274 m= 0 mr = 3 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1423 time to turn everything in is 0.3800000 number of dielectric boundary points 34409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16393 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) : 0.6929710 object centre at (A) : 27.19450 0.4495001 5.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6152068E-03 -4.0364668E-02 midg,1,midg; midg,igrid,midg 2.9161019E-02 -5.4630744E-03 1,midg,midg; igrid,midg,midg -3.5796233E-03 -2.7378971E-02 gauss-seidel spectral radius is 0.9988141 estimated iterations to convergence 230 setup time was (sec) 0.5900000 now iterating at: 07:59:58 rms-change max change #iterations 4.680035 176.0987 at 10iterations 2.292238 75.87523 at 20iterations 1.130154 36.21640 at 30iterations 0.5569267 18.02794 at 40iterations 0.2739915 8.231264 at 50iterations 0.1355684 4.048701 at 60iterations 6.6614687E-02 2.216798 at 70iterations 3.2718770E-02 1.050410 at 80iterations 1.6208671E-02 0.5617194 at 90iterations 7.9762368E-03 0.2505550 at 100iterations 3.9162938E-03 0.1092205 at 110iterations 1.9356114E-03 5.9735060E-02 at 120iterations finished qdiffx linear iterations at : 08:00:05 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.9356114E-03 5.9735060E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 08:00:06 7.773u 0.211s 0:08.24 96.8% 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 08:00:06 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2204 !!! WARNING: NDP 385 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.118370 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): 4.386000 50.00300 ymin,ymax (A): -25.23700 26.13600 zmin,zma (A): -19.74500 30.20500 x,y,z range (A): 45.61700 51.37300 49.95000 scale (grids/A): 3.118370 object centre (A): 27.19450 0.4495001 5.230000 number of atom coordinates read : 2204 total number of charged atoms : 2062 net assigned charge : -3.499991 assigned positive charge : 333.7805 centred at (gu) : 90.41869 94.73843 90.50671 assigned negative charge : -337.2808 centred at (gu) : 90.49715 95.14044 90.96583 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 178507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20468 grid for indexing accessible points = 1.400000 m= 95093 mr = 127987 m= 39244 mr = 78543 m= 11615 mr = 32110 m= 2337 mr = 9055 m= 322 mr = 1650 m= 24 mr = 193 m= 0 mr = 6 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 5009 time to turn everything in is 1.180000 number of dielectric boundary points 77598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 16496 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) : 2.078913 object centre at (A) : 27.19450 0.4495001 5.230000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7323486E-02 -0.2650715 midg,1,midg; midg,igrid,midg 0.8345321 6.3636847E-02 1,midg,midg; igrid,midg,midg -5.9950605E-02 -0.2509265 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 08:00:07 rms-change max change #iterations 10.51756 399.8914 at 10iterations 6.160996 149.0441 at 20iterations 3.594828 73.66718 at 30iterations 2.105040 52.52277 at 40iterations 1.229663 31.19077 at 50iterations 0.7181978 13.74831 at 60iterations 0.4191826 7.318381 at 70iterations 0.2443509 4.335399 at 80iterations 0.1423766 2.562700 at 90iterations 8.3080217E-02 1.447411 at 100iterations 4.8365012E-02 0.9328518 at 110iterations 2.8090807E-02 0.5503922 at 120iterations 1.6379235E-02 0.2843770 at 130iterations 9.5430715E-03 0.1693754 at 140iterations 5.5429055E-03 9.1622353E-02 at 150iterations 3.2348826E-03 5.7952881E-02 at 160iterations 1.8805120E-03 3.2375336E-02 at 170iterations 1.0966066E-03 1.9446850E-02 at 180iterations finished qdiffx linear iterations at : 08:00:19 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 1.0966066E-03 1.9446850E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:00:19 12.902u 0.208s 0:13.38 97.9% 0+0k 0+0io 0pf+0w