Tue Oct 11 00:18:17 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 Tue Oct 11 2011 at 00:18:17 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.5577053 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 0.5577053 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2409 net assigned charge : 7.906023 assigned positive charge : 386.2190 centred at (gu) : 88.87774 87.95837 89.67838 assigned negative charge : -378.3135 centred at (gu) : 88.88895 88.04020 89.51127 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5155 nv = 96 ne = 84 npr = 51181 no. pairs analyzed = 51181 no. exposed pairs = 3116 no. arc points = 21703 no. surface atoms = 1059 nbur = 1493 mkacc time = 0.1500000 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 = 1.540000 m= 195 mr = 2770 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3700000 number of dielectric boundary points 2574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6649 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7939122E-10 2.0068749E-09 midg,1,midg; midg,igrid,midg 2.3943261E-09 3.7006394E-11 1,midg,midg; igrid,midg,midg 1.1138478E-09 5.0823457E-10 gauss-seidel spectral radius is 0.9833797 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 00:18:18 rms-change max change #iterations 7.8878529E-02 13.81666 at 10iterations 6.4242124E-03 1.091358 at 20iterations 8.9938566E-04 0.2332306 at 30iterations 2.2107283E-04 5.8715820E-02 at 40iterations 5.6617107E-05 1.5224457E-02 at 50iterations finished qdiffx linear iterations at : 00:18:21 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 5.6617107E-05 1.5224457E-02 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 00:18:22 4.290u 0.225s 0:04.83 93.3% 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 00:18:22 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.673116 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 1.673116 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2409 net assigned charge : 7.906023 assigned positive charge : 386.2190 centred at (gu) : 86.63283 83.87474 89.03477 assigned negative charge : -378.3135 centred at (gu) : 86.66650 84.12031 88.53355 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 17701 mr = 39157 m= 1897 mr = 12595 m= 50 mr = 1027 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2841 time to turn everything in is 0.5500000 number of dielectric boundary points 23799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18583 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) : 0.5577053 object centre at (A) : 5.616500 76.33749 57.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2036736E-03 1.4843502E-02 midg,1,midg; midg,igrid,midg -1.4514833E-02 7.0858630E-03 1,midg,midg; igrid,midg,midg 3.7204898E-03 6.2645972E-03 gauss-seidel spectral radius is 0.9982228 estimated iterations to convergence 188 setup time was (sec) 0.9300000 now iterating at: 00:18:23 rms-change max change #iterations 3.216067 157.8770 at 10iterations 1.341110 56.93390 at 20iterations 0.5648254 23.05774 at 30iterations 0.2382344 8.727406 at 40iterations 0.1004429 4.183050 at 50iterations 4.2601399E-02 1.699146 at 60iterations 1.8120045E-02 0.6677094 at 70iterations 7.8166472E-03 0.3147812 at 80iterations 3.4424011E-03 0.1547928 at 90iterations 1.6139450E-03 7.5172424E-02 at 100iterations 8.1786932E-04 4.0626526E-02 at 110iterations 4.4618151E-04 2.4259567E-02 at 120iterations finished qdiffx linear iterations at : 00:18:31 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 4.4618151E-04 2.4259567E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 00:18:32 9.533u 0.243s 0:10.33 94.5% 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 00:18:32 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2552 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.509674 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): -19.81900 31.05200 ymin,ymax (A): 44.42100 108.2540 zmin,zma (A): 34.74300 79.35100 x,y,z range (A): 50.87100 63.83300 44.60800 scale (grids/A): 2.509674 object centre (A): 5.616500 76.33749 57.04700 number of atom coordinates read : 2552 total number of charged atoms : 2409 net assigned charge : 7.906023 assigned positive charge : 386.2190 centred at (gu) : 84.94917 80.81196 88.55209 assigned negative charge : -378.3135 centred at (gu) : 84.99969 81.18036 87.80014 start vw surface at 0.2100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 132096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21703 grid for indexing accessible points = 1.400000 m= 61160 mr = 95325 m= 17922 mr = 49162 m= 3111 mr = 13976 m= 175 mr = 2125 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 9696 time to turn everything in is 1.330000 number of dielectric boundary points 53808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19257 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) : 1.673116 object centre at (A) : 5.616500 76.33749 57.04700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4596996E-02 0.1769330 midg,1,midg; midg,igrid,midg -0.4588391 7.2404191E-02 1,midg,midg; igrid,midg,midg 1.1195408E-02 7.0057072E-02 gauss-seidel spectral radius is 0.9991315 estimated iterations to convergence 268 setup time was (sec) 1.700000 now iterating at: 00:18:34 rms-change max change #iterations 8.070115 310.2659 at 10iterations 4.441409 103.0420 at 20iterations 2.444746 62.11776 at 30iterations 1.344883 28.60883 at 40iterations 0.7348809 16.69088 at 50iterations 0.4038925 8.683203 at 60iterations 0.2209118 4.823987 at 70iterations 0.1214986 2.579417 at 80iterations 6.6536568E-02 1.409046 at 90iterations 3.6344003E-02 0.7618904 at 100iterations 2.0000568E-02 0.4700651 at 110iterations 1.1036453E-02 0.2428856 at 120iterations 6.1146310E-03 0.1270065 at 130iterations 3.4264706E-03 8.6997986E-02 at 140iterations 1.9657377E-03 5.5835724E-02 at 150iterations 1.1669487E-03 3.4351349E-02 at 160iterations 7.2339596E-04 2.0145416E-02 at 170iterations 4.7191742E-04 1.3828278E-02 at 180iterations finished qdiffx linear iterations at : 00:18:47 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 4.7191742E-04 1.3828278E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.14000 DelPhi exited at 00:18:48 15.144u 0.259s 0:15.71 97.9% 0+0k 0+0io 0pf+0w