Sun Oct 9 04:40:29 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 04:40:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 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: 0.6529354 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 0.6529354 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 374.1387 centred at (gu) : 90.02322 89.95070 89.99802 assigned negative charge : -367.6396 centred at (gu) : 90.14954 89.85386 89.95846 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7339 nv = 96 ne = 84 npr = 51284 no. pairs analyzed = 51284 no. exposed pairs = 3400 no. arc points = 23929 no. surface atoms = 1147 nbur = 1394 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 446 mr = 3827 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2265 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8693 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4620621E-09 1.9808631E-08 midg,1,midg; midg,igrid,midg -1.6454517E-09 2.8341326E-08 1,midg,midg; igrid,midg,midg 3.2970487E-08 -6.3728631E-09 gauss-seidel spectral radius is 0.9878442 estimated iterations to convergence 74 setup time was (sec) 0.5100000 now iterating at: 04:40:30 rms-change max change #iterations 0.1536707 22.73947 at 10iterations 1.5906475E-02 2.345001 at 20iterations 1.6636425E-03 0.2398090 at 30iterations 1.9550619E-04 2.8135300E-02 at 40iterations 3.9220016E-05 5.4969788E-03 at 50iterations finished qdiffx linear iterations at : 04:40:32 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.9220016E-05 5.4969788E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 04:40:32 3.157u 0.191s 0:03.62 92.2% 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 04:40:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 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: 1.958806 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 1.958806 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 374.1387 centred at (gu) : 90.06920 89.85138 89.99320 assigned negative charge : -367.6396 centred at (gu) : 90.44852 89.56155 89.87514 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23929 grid for indexing accessible points = 1.400000 m= 28440 mr = 53640 m= 4731 mr = 20026 m= 350 mr = 2706 m= 8 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 36002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18982 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) : 0.6529354 object centre at (A) : 12.47900 27.20750 0.9235001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0245493E-03 6.8334470E-05 midg,1,midg; midg,igrid,midg 5.0056963E-03 4.1296382E-02 1,midg,midg; igrid,midg,midg 3.4913708E-02 -6.9348221E-03 gauss-seidel spectral radius is 0.9987094 estimated iterations to convergence 220 setup time was (sec) 0.8600000 now iterating at: 04:40:34 rms-change max change #iterations 4.366757 177.2327 at 10iterations 2.088000 77.54599 at 20iterations 1.002672 30.91779 at 30iterations 0.4798119 15.28524 at 40iterations 0.2309820 7.655190 at 50iterations 0.1105021 3.199996 at 60iterations 5.3006280E-02 1.660416 at 70iterations 2.5339648E-02 0.9386404 at 80iterations 1.2162546E-02 0.3804045 at 90iterations 5.8112429E-03 0.1914186 at 100iterations 2.7910434E-03 8.4800720E-02 at 110iterations 1.3380565E-03 3.9104462E-02 at 120iterations finished qdiffx linear iterations at : 04:40:40 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.3380565E-03 3.9104462E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 04:40:41 7.826u 0.218s 0:08.34 96.2% 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 04:40:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2541 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.938210 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): -10.51200 35.47000 ymin,ymax (A): -5.4000020E-02 54.46900 zmin,zma (A): -25.29100 27.13800 x,y,z range (A): 45.98200 54.52300 52.42900 scale (grids/A): 2.938210 object centre (A): 12.47900 27.20750 0.9235001 number of atom coordinates read : 2541 total number of charged atoms : 2402 net assigned charge : 6.500035 assigned positive charge : 374.1387 centred at (gu) : 90.10367 89.77692 89.98962 assigned negative charge : -367.6396 centred at (gu) : 90.67275 89.34232 89.81266 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 182297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23929 grid for indexing accessible points = 1.400000 m= 91576 mr = 130355 m= 33560 mr = 73198 m= 8409 mr = 25930 m= 1286 mr = 5805 m= 132 mr = 792 m= 5 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 81131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19215 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) : 1.958806 object centre at (A) : 12.47900 27.20750 0.9235001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1964630 7.0599742E-02 midg,1,midg; midg,igrid,midg 4.1532189E-02 0.5301136 1,midg,midg; igrid,midg,midg 0.3399213 -8.1653275E-02 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.750000 now iterating at: 04:40:43 rms-change max change #iterations 10.34154 480.8774 at 10iterations 6.167092 160.8832 at 20iterations 3.659028 82.15965 at 30iterations 2.162954 48.23744 at 40iterations 1.271515 26.49231 at 50iterations 0.7468117 16.86324 at 60iterations 0.4375278 8.743617 at 70iterations 0.2560112 5.182803 at 80iterations 0.1494028 2.794044 at 90iterations 8.7211378E-02 1.642710 at 100iterations 5.0876167E-02 0.9626122 at 110iterations 2.9636653E-02 0.5507050 at 120iterations 1.7262723E-02 0.3311466 at 130iterations 1.0033024E-02 0.2073936 at 140iterations 5.8377609E-03 0.1086731 at 150iterations 3.4054262E-03 6.0495377E-02 at 160iterations 1.9774602E-03 3.6811829E-02 at 170iterations 1.1525718E-03 2.1699905E-02 at 180iterations finished qdiffx linear iterations at : 04:40:54 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.1525718E-03 2.1699905E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 04:40:54 13.068u 0.224s 0:13.56 97.9% 0+0k 0+0io 0pf+0w