Sat Oct 8 11:34:39 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+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 Sat Oct 8 2011 at 11:34:39 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5288176 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 0.5288176 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999949 assigned positive charge : 640.3110 centred at (gu) : 87.93203 90.00299 90.71687 assigned negative charge : -645.3135 centred at (gu) : 87.99899 90.13079 90.78214 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6867 nv = 96 ne = 84 npr = 94960 no. pairs analyzed = 94960 no. exposed pairs = 4402 no. arc points = 30332 no. surface atoms = 1521 nbur = 2745 mkacc time = 0.2200000 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= 228 mr = 3852 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.4400000 number of dielectric boundary points 3240 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3056 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3257394E-10 -5.8262734E-10 midg,1,midg; midg,igrid,midg 4.6198670E-10 -8.0234852E-10 1,midg,midg; igrid,midg,midg 2.9727631E-10 -2.9259856E-10 gauss-seidel spectral radius is 0.9816464 estimated iterations to convergence 61 setup time was (sec) 0.6700000 now iterating at: 11:34:40 rms-change max change #iterations 7.6975450E-02 12.95207 at 10iterations 4.9190479E-03 0.7548790 at 20iterations 3.5949596E-04 4.6096802E-02 at 30iterations 3.8056325E-05 5.7411194E-03 at 40iterations 5.7200218E-06 8.3541870E-04 at 50iterations finished qdiffx linear iterations at : 11:34:43 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.7200218E-06 8.3541870E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 11:34:43 3.473u 0.152s 0:04.32 83.7% 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 Sat Oct 8 2011 at 11:34:44 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.586453 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 1.586453 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999949 assigned positive charge : 640.3110 centred at (gu) : 83.79473 90.00781 92.14931 assigned negative charge : -645.3135 centred at (gu) : 83.99626 90.39246 92.34575 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21648 mr = 56705 m= 1969 mr = 14808 m= 48 mr = 951 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 3141 time to turn everything in is 0.5800000 number of dielectric boundary points 30076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 31274 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) : 0.5288176 object centre at (A) : 31.95500 12.91600 11.00150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0710128E-03 -1.9829744E-02 midg,1,midg; midg,igrid,midg 3.1224017E-03 -1.1321804E-02 1,midg,midg; igrid,midg,midg 3.0233467E-02 -7.4390355E-03 gauss-seidel spectral radius is 0.9981652 estimated iterations to convergence 185 setup time was (sec) 0.8700000 now iterating at: 11:34:45 rms-change max change #iterations 3.851785 149.2066 at 10iterations 1.591792 57.53094 at 20iterations 0.6651009 20.66064 at 30iterations 0.2766745 9.243267 at 40iterations 0.1149754 3.673628 at 50iterations 4.8086587E-02 1.533178 at 60iterations 1.9966247E-02 0.6088052 at 70iterations 8.3375210E-03 0.2837305 at 80iterations 3.4813965E-03 0.1226190 at 90iterations 1.4584694E-03 4.7880173E-02 at 100iterations 6.1040494E-04 1.9863367E-02 at 110iterations 2.5568157E-04 8.4495544E-03 at 120iterations finished qdiffx linear iterations at : 11:34:51 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 2.5568157E-04 8.4495544E-03 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 11:34:52 7.505u 0.170s 0:08.18 93.7% 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 Sat Oct 8 2011 at 11:34:52 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4266 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.379679 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): -1.705000 65.61500 ymin,ymax (A): -11.97100 37.80300 zmin,zma (A): -21.76700 43.77000 x,y,z range (A): 67.32000 49.77400 65.53700 scale (grids/A): 2.379679 object centre (A): 31.95500 12.91600 11.00150 number of atom coordinates read : 4266 total number of charged atoms : 4111 net assigned charge : -4.999949 assigned positive charge : 640.3110 centred at (gu) : 80.69183 90.01131 93.22360 assigned negative charge : -645.3135 centred at (gu) : 80.99430 90.58843 93.51852 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 184438 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30332 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 78549 mr = 138483 m= 19863 mr = 62825 m= 2946 mr = 14731 m= 196 mr = 1969 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 10267 time to turn everything in is 1.390000 number of dielectric boundary points 67904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 32825 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) : 1.586453 object centre at (A) : 31.95500 12.91600 11.00150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2375202 -0.3085735 midg,1,midg; midg,igrid,midg 1.4621046E-02 -0.1564585 1,midg,midg; igrid,midg,midg 0.8926376 -0.4097079 gauss-seidel spectral radius is 0.9991450 estimated iterations to convergence 270 setup time was (sec) 1.700000 now iterating at: 11:34:54 rms-change max change #iterations 9.970696 314.0453 at 10iterations 5.571435 128.5256 at 20iterations 3.115279 62.48276 at 30iterations 1.733910 36.44166 at 40iterations 0.9613044 19.83015 at 50iterations 0.5327730 10.80502 at 60iterations 0.2942697 5.473876 at 70iterations 0.1629953 2.998408 at 80iterations 9.0160020E-02 1.683205 at 90iterations 4.9698427E-02 1.026875 at 100iterations 2.7508972E-02 0.5579081 at 110iterations 1.5186880E-02 0.2983246 at 120iterations 8.3970688E-03 0.1551982 at 130iterations 4.6253921E-03 8.4197998E-02 at 140iterations 2.5567987E-03 4.7942162E-02 at 150iterations 1.4101956E-03 2.4642944E-02 at 160iterations 7.7962124E-04 1.5047073E-02 at 170iterations 4.3157313E-04 8.0757141E-03 at 180iterations finished qdiffx linear iterations at : 11:35:09 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 4.3157313E-04 8.0757141E-03 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 11:35:10 13.137u 0.252s 0:18.04 74.1% 0+0k 0+0io 0pf+0w