Mon Oct 10 17:01:20 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 Mon Oct 10 2011 at 17:01:20 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 = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6050614 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 0.6050614 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.999963 assigned positive charge : 445.3379 centred at (gu) : 89.17084 89.68586 89.20750 assigned negative charge : -449.3391 centred at (gu) : 89.05811 89.57628 89.09298 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7277 nv = 96 ne = 84 npr = 60022 no. pairs analyzed = 60022 no. exposed pairs = 3831 no. arc points = 26957 no. surface atoms = 1300 nbur = 1676 mkacc time = 9.9999994E-02 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 = 1.456000 m= 318 mr = 3824 m= 0 mr = 29 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2200000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9084 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1068690E-09 3.0600003E-09 midg,1,midg; midg,igrid,midg -7.8965314E-09 3.2018266E-09 1,midg,midg; igrid,midg,midg -9.0737489E-09 2.9626634E-09 gauss-seidel spectral radius is 0.9858969 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 17:01:20 rms-change max change #iterations 0.1166478 17.40278 at 10iterations 1.0324614E-02 1.347468 at 20iterations 9.0180372E-04 0.1622219 at 30iterations 7.7230921E-05 1.1222839E-02 at 40iterations 6.7091928E-06 1.0337830E-03 at 50iterations finished qdiffx linear iterations at : 17:01:23 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.7091928E-06 1.0337830E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 17:01:24 3.478u 0.161s 0:04.46 81.3% 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 Mon Oct 10 2011 at 17:01:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.815184 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 1.815184 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.999963 assigned positive charge : 445.3379 centred at (gu) : 87.51141 89.05658 87.62164 assigned negative charge : -449.3391 centred at (gu) : 87.17387 88.72839 87.27866 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26957 grid for indexing accessible points = 1.400000 m= 26206 mr = 54268 m= 3275 mr = 18397 m= 112 mr = 1823 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1284 time to turn everything in is 0.4000000 number of dielectric boundary points 34587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 22159 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) : 0.6050614 object centre at (A) : 20.10950 14.97200 25.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6499722E-03 2.4136871E-02 midg,1,midg; midg,igrid,midg -2.2531467E-02 8.2157115E-03 1,midg,midg; igrid,midg,midg -4.4483554E-02 2.3654144E-02 gauss-seidel spectral radius is 0.9985392 estimated iterations to convergence 207 setup time was (sec) 0.6200000 now iterating at: 17:01:25 rms-change max change #iterations 4.164417 187.4214 at 10iterations 1.892048 62.58031 at 20iterations 0.8577670 32.76890 at 30iterations 0.3916242 12.07506 at 40iterations 0.1780734 5.514193 at 50iterations 8.1229396E-02 2.726013 at 60iterations 3.6914211E-02 1.125702 at 70iterations 1.6901758E-02 0.5450532 at 80iterations 7.7020666E-03 0.2392521 at 90iterations 3.5162894E-03 0.1176338 at 100iterations 1.6027137E-03 4.7937393E-02 at 110iterations 7.3019497E-04 2.1474838E-02 at 120iterations finished qdiffx linear iterations at : 17:01:32 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 7.3019497E-04 2.1474838E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 17:01:33 7.976u 0.176s 0:08.50 95.7% 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 Mon Oct 10 2011 at 17:01:33 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 = 2976 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.722776 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): -8.372000 48.59100 ymin,ymax (A): -8.696000 38.64000 zmin,zma (A): -3.478000 55.35900 x,y,z range (A): 56.96301 47.33600 58.83700 scale (grids/A): 2.722776 object centre (A): 20.10950 14.97200 25.94050 number of atom coordinates read : 2976 total number of charged atoms : 2834 net assigned charge : -3.999963 assigned positive charge : 445.3379 centred at (gu) : 86.26684 88.58466 86.43232 assigned negative charge : -449.3391 centred at (gu) : 85.76070 88.09250 85.91801 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26957 grid for indexing accessible points = 1.400000 m= 87611 mr = 132245 m= 27970 mr = 70164 m= 5449 mr = 21435 m= 537 mr = 3875 m= 18 mr = 292 m= 0 mr = 3 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 4241 time to turn everything in is 0.9900000 number of dielectric boundary points 77907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 22670 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) : 1.815184 object centre at (A) : 20.10950 14.97200 25.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1363310 0.4068797 midg,1,midg; midg,igrid,midg -0.2262426 0.1190704 1,midg,midg; igrid,midg,midg -0.5100521 0.4120305 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 1.220000 now iterating at: 17:01:34 rms-change max change #iterations 10.19050 328.7159 at 10iterations 5.978326 147.8114 at 20iterations 3.478568 94.88175 at 30iterations 2.011927 42.79748 at 40iterations 1.161434 24.09982 at 50iterations 0.6716650 14.60168 at 60iterations 0.3854568 8.386992 at 70iterations 0.2213730 4.198219 at 80iterations 0.1267898 2.458763 at 90iterations 7.2787181E-02 1.433325 at 100iterations 4.1705798E-02 0.7923412 at 110iterations 2.3935435E-02 0.4373360 at 120iterations 1.3688200E-02 0.2316256 at 130iterations 7.8344112E-03 0.1417542 at 140iterations 4.4846237E-03 7.7630997E-02 at 150iterations 2.5671530E-03 5.1033974E-02 at 160iterations 1.4691439E-03 2.6551723E-02 at 170iterations 8.4296311E-04 1.4520645E-02 at 180iterations finished qdiffx linear iterations at : 17:01:46 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 8.4296311E-04 1.4520645E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 17:01:46 12.680u 0.223s 0:13.27 97.2% 0+0k 0+0io 0pf+0w