Sat Oct 8 17:26:09 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 17:26:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 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: 0.5390428 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 0.5390428 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999989 assigned positive charge : 509.7215 centred at (gu) : 90.42058 91.51186 90.46617 assigned negative charge : -511.7228 centred at (gu) : 90.44663 91.46703 90.42945 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6179 nv = 96 ne = 84 npr = 69584 no. pairs analyzed = 69584 no. exposed pairs = 4046 no. arc points = 27995 no. surface atoms = 1379 nbur = 2002 mkacc time = 0.2000000 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= 224 mr = 3344 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2805 ## 395 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8078415E-10 1.3046100E-10 midg,1,midg; midg,igrid,midg -2.4939062E-10 2.4200930E-10 1,midg,midg; igrid,midg,midg 4.7419062E-11 -2.8061345E-10 gauss-seidel spectral radius is 0.9822837 estimated iterations to convergence 62 setup time was (sec) 0.6900000 now iterating at: 17:26:10 rms-change max change #iterations 7.6706290E-02 13.37355 at 10iterations 4.9535916E-03 0.7861023 at 20iterations 3.6928605E-04 5.9496969E-02 at 30iterations 4.6259473E-05 1.1013031E-02 at 40iterations 9.6700078E-06 2.3612976E-03 at 50iterations finished qdiffx linear iterations at : 17:26:13 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 9.6700078E-06 2.3612976E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 17:26:14 4.162u 0.260s 0:04.70 94.0% 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 17:26:14 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 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: 1.617128 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 1.617128 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999989 assigned positive charge : 509.7215 centred at (gu) : 91.26099 94.53448 91.39790 assigned negative charge : -511.7228 centred at (gu) : 91.33967 94.40065 91.28810 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68781 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27995 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21061 mr = 47603 m= 2128 mr = 14649 m= 49 mr = 1026 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 566 time to turn everything in is 0.6300000 number of dielectric boundary points 28741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24672 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) : 0.5390428 object centre at (A) : 14.50150 -5.338500 9.063501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0548736E-03 4.0095942E-03 midg,1,midg; midg,igrid,midg 4.6938946E-03 5.4191374E-03 1,midg,midg; igrid,midg,midg -4.0588127E-03 -1.1992580E-02 gauss-seidel spectral radius is 0.9981776 estimated iterations to convergence 186 setup time was (sec) 0.9200000 now iterating at: 17:26:15 rms-change max change #iterations 3.500812 166.2406 at 10iterations 1.461941 47.45247 at 20iterations 0.6093627 22.71717 at 30iterations 0.2532583 8.809096 at 40iterations 0.1055040 3.820869 at 50iterations 4.4075511E-02 1.454236 at 60iterations 1.8414794E-02 0.6367798 at 70iterations 7.6703476E-03 0.3176880 at 80iterations 3.2127227E-03 0.1257134 at 90iterations 1.3423454E-03 4.5124054E-02 at 100iterations 5.6235329E-04 2.0115376E-02 at 110iterations 2.3713740E-04 9.0284348E-03 at 120iterations finished qdiffx linear iterations at : 17:26:23 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 2.3713740E-04 9.0284348E-03 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 17:26:24 9.309u 0.292s 0:09.87 97.1% 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 Sat Oct 8 2011 at 17:26:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3381 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: 2.425692 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): -14.09700 43.10000 ymin,ymax (A): -38.36000 27.68300 zmin,zma (A): -15.77700 33.90400 x,y,z range (A): 57.19700 66.04300 49.68100 scale (grids/A): 2.425692 object centre (A): 14.50150 -5.338500 9.063501 number of atom coordinates read : 3381 total number of charged atoms : 3235 net assigned charge : -1.999989 assigned positive charge : 509.7215 centred at (gu) : 91.89102 96.80154 92.09683 assigned negative charge : -511.7228 centred at (gu) : 92.00938 96.60088 91.93188 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 159928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27995 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 73778 mr = 116326 m= 20658 mr = 58731 m= 3355 mr = 15628 m= 210 mr = 2187 m= 2 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1924 time to turn everything in is 1.540000 number of dielectric boundary points 64977 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 25848 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) : 1.617128 object centre at (A) : 14.50150 -5.338500 9.063501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1051955 6.1545160E-02 midg,1,midg; midg,igrid,midg 0.1169344 0.2014729 1,midg,midg; igrid,midg,midg -9.1140196E-02 -0.1611080 gauss-seidel spectral radius is 0.9991369 estimated iterations to convergence 269 setup time was (sec) 1.850000 now iterating at: 17:26:26 rms-change max change #iterations 9.115149 252.5488 at 10iterations 5.134049 111.4357 at 20iterations 2.862679 58.90376 at 30iterations 1.590982 33.48797 at 40iterations 0.8837572 18.78653 at 50iterations 0.4880735 10.02573 at 60iterations 0.2698430 5.935501 at 70iterations 0.1486653 3.194704 at 80iterations 8.2032979E-02 1.935772 at 90iterations 4.5167524E-02 0.8791924 at 100iterations 2.4878746E-02 0.5358448 at 110iterations 1.3685036E-02 0.3037329 at 120iterations 7.5297933E-03 0.1400175 at 130iterations 4.1483543E-03 7.8456998E-02 at 140iterations 2.2823075E-03 4.9113274E-02 at 150iterations 1.2589627E-03 2.6851654E-02 at 160iterations 6.9752341E-04 1.2865067E-02 at 170iterations 3.8788305E-04 8.3394051E-03 at 180iterations finished qdiffx linear iterations at : 17:26:39 total time elapsed so far: 15.28000 # loops : 180 mean,max change (kT/e) : 3.8788305E-04 8.3394051E-03 energy calculations done at 15.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 17:26:40 15.465u 0.296s 0:16.17 97.4% 0+0k 0+0io 0pf+0w