Tue Oct 11 05:12:18 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 05:12:18 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7155203 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 0.7155203 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1907 net assigned charge : 5.931010 assigned positive charge : 309.1391 centred at (gu) : 89.79780 89.15032 90.20436 assigned negative charge : -303.2081 centred at (gu) : 89.66905 89.18310 90.24929 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7137 nv = 96 ne = 84 npr = 39677 no. pairs analyzed = 39677 no. exposed pairs = 2468 no. arc points = 16832 no. surface atoms = 840 nbur = 1173 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4141 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3000000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1564 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7754 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2937873E-08 3.5893496E-08 midg,1,midg; midg,igrid,midg 9.3148373E-08 3.5751171E-08 1,midg,midg; igrid,midg,midg -1.5077108E-08 1.2842202E-07 gauss-seidel spectral radius is 0.9898107 estimated iterations to convergence 81 setup time was (sec) 0.5600000 now iterating at: 05:12:19 rms-change max change #iterations 0.2132183 29.27324 at 10iterations 2.6813060E-02 4.434212 at 20iterations 3.6171104E-03 0.5320005 at 30iterations 5.4242613E-04 6.9036484E-02 at 40iterations 1.1293543E-04 1.4530182E-02 at 50iterations finished qdiffx linear iterations at : 05:12:22 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.1293543E-04 1.4530182E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 05:12:23 3.999u 0.260s 0:04.55 93.4% 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 05:12:23 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.146561 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 2.146561 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1907 net assigned charge : 5.931010 assigned positive charge : 309.1391 centred at (gu) : 89.39339 87.45097 90.61304 assigned negative charge : -303.2081 centred at (gu) : 89.00715 87.54954 90.74811 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75064 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 31205 mr = 53471 m= 6419 mr = 24155 m= 653 mr = 4429 m= 18 mr = 361 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.7000000 number of dielectric boundary points 30944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15151 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) : 0.7155203 object centre at (A) : 2.454500 9.166000 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6784653E-02 5.2384961E-02 midg,1,midg; midg,igrid,midg 3.8122687E-02 4.5792549E-03 1,midg,midg; igrid,midg,midg 2.0325614E-02 2.9473800E-02 gauss-seidel spectral radius is 0.9988481 estimated iterations to convergence 233 setup time was (sec) 1.010000 now iterating at: 05:12:24 rms-change max change #iterations 4.655735 175.8277 at 10iterations 2.323083 71.28564 at 20iterations 1.163902 35.13254 at 30iterations 0.5799595 22.08759 at 40iterations 0.2903239 8.917500 at 50iterations 0.1450557 4.241185 at 60iterations 7.2543435E-02 2.278134 at 70iterations 3.6138028E-02 1.112762 at 80iterations 1.8084018E-02 0.6470248 at 90iterations 9.1057578E-03 0.2715225 at 100iterations 4.5924988E-03 0.1485901 at 110iterations 2.3457438E-03 7.0568085E-02 at 120iterations finished qdiffx linear iterations at : 05:12:32 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 2.3457438E-03 7.0568085E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 05:12:33 9.462u 0.269s 0:10.37 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 Tue Oct 11 2011 at 05:12:33 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.219841 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): -18.97400 23.88300 ymin,ymax (A): -10.34200 28.67400 zmin,zma (A): -2.165000 47.58900 x,y,z range (A): 42.85700 39.01600 49.75400 scale (grids/A): 3.219841 object centre (A): 2.454500 9.166000 22.71200 number of atom coordinates read : 2013 total number of charged atoms : 1907 net assigned charge : 5.931010 assigned positive charge : 309.1391 centred at (gu) : 89.09022 86.17642 90.91960 assigned negative charge : -303.2081 centred at (gu) : 88.51074 86.32432 91.12218 start vw surface at 0.1400000 fill in re-entrant regions at 0.9700000 boundary points on vw surface= 172787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 96021 mr = 128569 m= 40730 mr = 80606 m= 12242 mr = 33975 m= 2677 mr = 9685 m= 343 mr = 2048 m= 9 mr = 236 m= 0 mr = 4 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1260 time to turn everything in is 2.220000 number of dielectric boundary points 69686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 15256 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) : 2.146561 object centre at (A) : 2.454500 9.166000 22.71200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2638877 0.6153856 midg,1,midg; midg,igrid,midg 0.2848333 1.9462053E-02 1,midg,midg; igrid,midg,midg 0.3784850 0.2394485 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 2.540000 now iterating at: 05:12:36 rms-change max change #iterations 10.25376 275.4754 at 10iterations 6.070768 135.2499 at 20iterations 3.584427 73.67496 at 30iterations 2.116148 40.89025 at 40iterations 1.249755 28.30416 at 50iterations 0.7334222 13.95143 at 60iterations 0.4311326 8.757694 at 70iterations 0.2533237 4.411982 at 80iterations 0.1489997 3.001747 at 90iterations 8.7600708E-02 1.728241 at 100iterations 5.1444560E-02 0.8497391 at 110iterations 3.0390322E-02 0.5278625 at 120iterations 1.8097484E-02 0.3177071 at 130iterations 1.0958613E-02 0.2051601 at 140iterations 6.8087033E-03 0.1280556 at 150iterations 4.4014696E-03 8.3106995E-02 at 160iterations 3.0056480E-03 5.2433014E-02 at 170iterations 2.1748322E-03 3.8776398E-02 at 180iterations finished qdiffx linear iterations at : 05:12:49 total time elapsed so far: 16.09000 # loops : 180 mean,max change (kT/e) : 2.1748322E-03 3.8776398E-02 energy calculations done at 16.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 05:12:50 16.265u 0.316s 0:16.98 97.5% 0+0k 0+0io 0pf+0w